I HAVE A 1998 FORD EXPLORER AND IT HESITATES ON ACCELERATION AND SOMETIMES IDLES ROUGH. I REPLACED THE SPARK PLUGS, WIRES, AND THE COIL PACK AND STILL HAVE THIS PROBLEMS. THE CODES SHOW MISSFIRES IN BANK 3 AND 5 AND POSSIBLE MAF. WHAT SHOULD I DO?

Are you sure the spark plug wires are on the correct spark plug? Recheck the firing order and spark plug wires. Additionally check timing on distrubutor

Did you clean out spark plug wells? Sometimes when removing intake, coolant leaks into spark plug wells shorting out spark to cylinder wall instead of plug..check for coolant traces on coils.Could have weak coil.

Wow! So many things can cause hesitation or miss. Did you run the OBD II scan? Auto-Zone will scan it for you. Usually on an older car,unless the spark plug wiring has been recently replaced,you need to do that too.
Then you have a lot of age on the coil pack also.Also clean your MAF sensor and your idle air control valve at the throttle gizmo.
Describe the hesitation a little more. don-ohio (:^)

it could be just about anything. first start by checking plugs, wires, and coil.Engine hesitation, which is normally most apparent during acceleration, is a condition that often results from either abnormal fuel flow to an engine or abnormal electrical conduction to a vehicle's spark plugs. Bad spark plug wires, whether they degrade internally or develop cracks and breaks in their outer coverings that cause electrical interference, can cause an engine to hesitate. Engine Surging, Engine surging is a common symptom of bad spark plug wires, especially if the wires have cracks or breaks in their outside insulation, heres the symtoms for a bad fuel filter. Engine Hesitation, Engine Stalling, Rough Engine Idle, Reduced Engine Power. if really plugged it will stop fuel flow and car will not start. just give it a good tuneup, and go from there! good-day!

The coil pack is held on by 2 5.5mm bolts. Take the bolt's out and the coil just pulls up.
I take it the spark plug wires are good?

New plugs and wires?

Double check to make sure that you've got the routing and firing order right... if you have 2 switched, the car may still idle well but then pop and sputter on harder acceleration.

The next step would be to run some "Complete Fuel System Cleaner"... If that's the problem, you should see results within 20 miles or so.

Did you try changing plugs and WIRES!! wires are the most common cause of this problem, under load if you have a bad cracked wire it will "leak" the spark causing a weaker spark there for making your spark at the plug weak not burning the entire charge in the cylinder. If this still doesn't solve your problem being the cheap way (im sure it may fix it) try by changing your coil packs let me know what happens. If all else fails you may have a sloppy injector

check plugs, wires, and coils for proper spark.

You have a hesitation. A hesitation is cause be either:
1. bad spark plug
2. bad spark plug wire
3. bad or leaky or plugged injector
4. timing is off
5. leaky vacuum hose