On an 05 deluxe intermitten noise from engine upon throttle and sometimes while idling sounds almost like a rod knocking but is smooth as silk while at hyway speeds

Not sure what you mean by opening the engine.

The combustion process of a diesel is not the smooth burn and increase in pressure of a petrol engine but is virtually an explosion causing a sudden rise in cylinder pressure. This is the source of the typical diesel knock and is more pronounced in some engines and some injection systems, especially when accelerating. It can be scary for those unfamiliar.
Electronic control tends to soften the noise.

Knocking might be the result of a mechanical problem (piston, connecting rod bearings, etc.) but if these things have been eliminated other causes of excess knocking can be excessive injection timing advance, dribbling injectors, bad spray patterns...

If its a knocking sound:

A KNOCKING SOUND IN THE ENGINE IS MOST LIKELY CAUSED BY ONE OF THE FOLLOWING
1. PISTON SLAP: Makes a sharp metallic noise. Idle engine and short out each cylinder plug. The noise will disappear when plug with bad piston is shorted. Noise will also disappear at acceleration. This can be caused by worn or out of round cylinder, or broken piston ring. Correct problem by re-boring cylinder and/or replacing piston.
2. VALVE NOISE: Makes clicking or rattle noise. Caused by excessive wear on valve stem or lifter, out of adjustment, or stuck valve. Correct by adjusting valve clearance, replace worn valve or lifter, regrind cam, replace valve guide and /or valve. A stuck valve can sometimes be loosened by passing oil through the carburetor while engine is running.

3. ROD BEARING KNOCK: Makes sharp metallic noise similar to a piston slap. Detection is opposite of piston slap. Rod knock is not heard at idle. Knock becomes louder as engine speed is increased. Caused by excessive rod bearing clearance. Correct by adjusting rod bearing clearance to .0015 inches by removing shims. May require re-pouring rod bearing.
4. REAR MAIN BEARING KNOCK: Makes dull knocking or thud noise. Detected at speeds between 20 and 50 MPH. Knock will normally decrease or disappear while pulling or decelerating. Noise will be detected the loudest at normal driving speed, when not pulling or decelerating. Correct by adjusting bearing clearance to .001 to .0015 inches. If knock is excessive, crank should be checked for out of roundness. May need to re-pour all main bearings to correct.
5. TIMING GEAR KNOCK: usually the most difficult to diagnose. If gear is loose or badly worn it will knock in all ranges. Run engine slightly above idle speed. Slowly open and close throttle. Knock will continue to be present, but just as engine slows down knock will become a slight rattle. Remove timing pin and reinsert into timing hole on timing gear cover. Press timing pin tightly against timing gear and accelerate slightly above idle. Knock will significantly be reduced or disappear. Correct by replacing both timing gear and crank gear as a matched set. The two gears should have a backlash clearance of .003 to .004. If more than .009 inch backlash, an oversize (.005) timing gear should be installed.
6. WRIST PIN SLAP: This can not be detected by shorting out the cylinder plugs. Rapidly accelerate and decelerate the engine speed. The engine will pass through a certain speed range when the wrist pin will rattle at about the same pitch as a valve tappet noise. This can be corrected by installing a new wrist pin bushing in the rod or new wrist pin f badly worn. Wrist pin should fit the piston and connecting rod with a tight metal to metal fit. The pin can be pushed into the piston and rod with a slight pressure of the hand. Pin to rod clearance is .0003 to .0005 inches.

TROUBLESHOOTING ENGINE NOISES
A KNOCKING SOUND IN THE ENGINE IS MOST LIKELY CAUSED BY ONE OF THE FOLLOWING
1. PISTON SLAP: Makes a sharp metallic noise. Idle engine and short out each cylinder plug. The noise will disappear when plug with bad piston is shorted. Noise will also disappear at acceleration. This can be caused by worn or out of round cylinder, or broken piston ring. Correct problem by re-boring cylinder and/or replacing piston.
2. VALVE NOISE: Makes clicking or rattle noise. Caused by excessive wear on valve stem or lifter, out of adjustment, or stuck valve. Correct by adjusting valve clearance, replace worn valve or lifter, regrind cam, replace valve guide and /or valve. A stuck valve can sometimes be loosened by passing oil through the carburetor while engine is running.

3. ROD BEARING KNOCK: Makes sharp metallic noise similar to a piston slap. Detection is opposite of piston slap. Rod knock is not heard at idle. Knock becomes louder as engine speed is increased. Caused by excessive rod bearing clearance. Correct by adjusting rod bearing clearance to .0015 inches by removing shims. May require re-pouring rod bearing.
4. REAR MAIN BEARING KNOCK: Makes dull knocking or thud noise. Detected at speeds between 20 and 50 MPH. Knock will normally decrease or disappear while pulling or decelerating. Noise will be detected the loudest at normal driving speed, when not pulling or decelerating. Correct by adjusting bearing clearance to .001 to .0015 inches. If knock is excessive, crank should be checked for out of roundness. May need to re-pour all main bearings to correct.
5. TIMING GEAR KNOCK: usually the most difficult to diagnose. If gear is loose or badly worn it will knock in all ranges. Run engine slightly above idle speed. Slowly open and close throttle. Knock will continue to be present, but just as engine slows down knock will become a slight rattle. Remove timing pin and reinsert into timing hole on timing gear cover. Press timing pin tightly against timing gear and accelerate slightly above idle. Knock will significantly be reduced or disappear. Correct by replacing both timing gear and crank gear as a matched set. The two gears should have a backlash clearance of .003 to .004. If more than .009 inch backlash, an oversize (.005) timing gear should be installed.
6. WRIST PIN SLAP: This can not be detected by shorting out the cylinder plugs. Rapidly accelerate and decelerate the engine speed. The engine will pass through a certain speed range when the wrist pin will rattle at about the same pitch as a valve tappet noise. This can be corrected by installing a new wrist pin bushing in the rod or new wrist pin f badly worn. Wrist pin should fit the piston and connecting rod with a tight metal to metal fit. The pin can be pushed into the piston and rod with a slight pressure of the hand. Pin to rod clearance is .0003 to .0005 inches.

A KNOCKING SOUND IN THE ENGINE IS MOST LIKELY CAUSED BY ONE OF THE FOLLOWING
1. PISTON SLAP: Makes a sharp metallic noise. Idle engine and short out each cylinder plug. The noise will disappear when plug with bad piston is shorted. Noise will also disappear at acceleration. This can be caused by worn or out of round cylinder, or broken piston ring. Correct problem by re-boring cylinder and/or replacing piston.
2. VALVE NOISE: Makes clicking or rattle noise. Caused by excessive wear on valve stem or lifter, out of adjustment, or stuck valve. Correct by adjusting valve clearance, replace worn valve or lifter, regrind cam, replace valve guide and /or valve. A stuck valve can sometimes be loosened by passing oil through the carburetor while engine is running.

3. ROD BEARING KNOCK: Makes sharp metallic noise similar to a piston slap. Detection is opposite of piston slap. Rod knock is not heard at idle. Knock becomes louder as engine speed is increased. Caused by excessive rod bearing clearance. Correct by adjusting rod bearing clearance to .0015 inches by removing shims. May require re-pouring rod bearing.
4. REAR MAIN BEARING KNOCK: Makes dull knocking or thud noise. Detected at speeds between 20 and 50 MPH. Knock will normally decrease or disappear while pulling or decelerating. Noise will be detected the loudest at normal driving speed, when not pulling or decelerating. Correct by adjusting bearing clearance to .001 to .0015 inches. If knock is excessive, crank should be checked for out of roundness. May need to re-pour all main bearings to correct.
5. TIMING GEAR KNOCK: usually the most difficult to diagnose. If gear is loose or badly worn it will knock in all ranges. Run engine slightly above idle speed. Slowly open and close throttle. Knock will continue to be present, but just as engine slows down knock will become a slight rattle. Remove timing pin and reinsert into timing hole on timing gear cover. Press timing pin tightly against timing gear and accelerate slightly above idle. Knock will significantly be reduced or disappear. Correct by replacing both timing gear and crank gear as a matched set. The two gears should have a backlash clearance of .003 to .004. If more than .009 inch backlash, an oversize (.005) timing gear should be installed.
6. WRIST PIN SLAP: This can not be detected by shorting out the cylinder plugs. Rapidly accelerate and decelerate the engine speed. The engine will pass through a certain speed range when the wrist pin will rattle at about the same pitch as a valve tappet noise. This can be corrected by installing a new wrist pin bushing in the rod or new wrist pin f badly worn. Wrist pin should fit the piston and connecting rod with a tight metal to metal fit. The pin can be pushed into the piston and rod with a slight pressure of the hand. Pin to rod clearance is .0003 to .0005 inches.

A KNOCKING SOUND IN THE ENGINE IS MOST LIKELY CAUSED BY ONE OF THE FOLLOWING
1. PISTON SLAP: Makes a sharp metallic noise. Idle engine and short out each cylinder plug. The noise will disappear when plug with bad piston is shorted. Noise will also disappear at acceleration. This can be caused by worn or out of round cylinder, or broken piston ring. Correct problem by re-boring cylinder and/or replacing piston.
2. VALVE NOISE: Makes clicking or rattle noise. Caused by excessive wear on valve stem or lifter, out of adjustment, or stuck valve. Correct by adjusting valve clearance, replace worn valve or lifter, regrind cam, replace valve guide and /or valve. A stuck valve can sometimes be loosened by passing oil through the carburetor while engine is running.

3. ROD BEARING KNOCK: Makes sharp metallic noise similar to a piston slap. Detection is opposite of piston slap. Rod knock is not heard at idle. Knock becomes louder as engine speed is increased. Caused by excessive rod bearing clearance. Correct by adjusting rod bearing clearance to .0015 inches by removing shims. May require re-pouring rod bearing.
4. REAR MAIN BEARING KNOCK: Makes dull knocking or thud noise. Detected at speeds between 20 and 50 MPH. Knock will normally decrease or disappear while pulling or decelerating. Noise will be detected the loudest at normal driving speed, when not pulling or decelerating. Correct by adjusting bearing clearance to .001 to .0015 inches. If knock is excessive, crank should be checked for out of roundness. May need to re-pour all main bearings to correct.
5. TIMING GEAR KNOCK: usually the most difficult to diagnose. If gear is loose or badly worn it will knock in all ranges. Run engine slightly above idle speed. Slowly open and close throttle. Knock will continue to be present, but just as engine slows down knock will become a slight rattle. Remove timing pin and reinsert into timing hole on timing gear cover. Press timing pin tightly against timing gear and accelerate slightly above idle. Knock will significantly be reduced or disappear. Correct by replacing both timing gear and crank gear as a matched set. The two gears should have a backlash clearance of .003 to .004. If more than .009 inch backlash, an oversize (.005) timing gear should be installed.
6. WRIST PIN SLAP: This can not be detected by shorting out the cylinder plugs. Rapidly accelerate and decelerate the engine speed. The engine will pass through a certain speed range when the wrist pin will rattle at about the same pitch as a valve tappet noise. This can be corrected by installing a new wrist pin bushing in the rod or new wrist pin f badly worn. Wrist pin should fit the piston and connecting rod with a tight metal to metal fit. The pin can be pushed into the piston and rod with a slight pressure of the hand. Pin to rod clearance is .0003 to .0005 inches.

Not sure on model but to me sounds like its a dodgey valve lifter when the seals start to go they cannot hold the oil and when there under pressure they basically empty them selves hence when you turn the engine off and restart you get a rattle sound untill the valve fills again as long as the cars running ok leave it untill you have to replace them unless there easy to do sone are sone are a pain

Hey Kimberly... First... is the noise a high pitched ticking or a lower pitched knocking or clunking?? ...this is IMPORTANT>>
Reply to me on here..please...

could be a cracked exhaust manifold or manifold gasket.

check engine oil pressure first .how is the oil pressure? is it low ?
when you raise the engine speed and bring it down to idle fast ---do you hear the noise? Do not do that at high speed and only once or twice or may do more damage to the engine. If you hear the noise ---"knocking" ---than it sounds like a loose connecting rod bearing ----means you need your engine rebuilt or replaced.

Make sure you have enough oil in the engine (though it's likely too late) If you have knocking and oil light on, sorry to say, you likely have lost a rod or crank main bearing (engine needs to come out of car and completely apart (very expensive) Options are a re-manufactured or scrapyard replacement.