Engine runs rough at idle, but smooths out in drive after about 40 mph and then get rough and bucks in overdrive

replace no 6 injector
check injector wires and connections

You can try a drive cycle, see if it helps? There may be an idle relearn, if just idle issue? Usually it will relearn idle on its own by driving.
Drive Cycle Recommendations:

1. Most OBDII monitors will complete more readily using a "steady foot" driving style during cruise or acceleration modes. Operating the throttle in a "smooth" fashion will minimize the time required for monitor completion.
2. Fuel tank level should be between 1/2 and 3/4 fill with 3/4 fill being the most desirable.
3. The Evaporative Monitor can only operate during the first 30 minutes of engine operation. When executing the procedure for this monitor, stay in part throttle mode and drive in a smooth fashion to minimize "fuel slosh".

WARNING
STRICT OBSERVANCE OF POSTED SPEED LIMITS AND ATTENTION TO DRIVING CONDITIONS ARE MANDATORY WHEN PROCEEDING THROUGH THE FOLLOWING DRIVE CYCLES.
For best results, follow each of the following steps as accurately as possible:
OBDII Monitor
Exercised Drive Cycle Procedure
Purpose of
Drive Cycle Procedure Drive Cycle
Preparation 1. Install scan tool. Turn key on with the engine off. Cycle key off, then on. Select appropriate Vehicle & Engine qualifier. Clear all DTC's/ Perform a PCM Reset. Bypasses engine soak timer. Resets OBDII Monitor status. 2. Begin to monitor the following PIDs: ECT, EVAPDC, FLI (if available) and TP MODE.
Start vehicle WITHOUT returning to Key Off. 3. Idle vehicle for 15 seconds. Drive at 64 Km/h (40 MPH) until ECT is at least 76.7°C (170° F). Prep for Monitor Entry 4. Is IAT within 4.4 to 37.8°C (40 to 100° F)? If Not, complete the following steps but, note that step 14 will be required to "bypass " the Evap monitor and clear the P1000. Engine warm-up and provide IAT input to the PCM. HEGO 5. Cruise at 64 Km/h (40 MPH) for up to 4 minutes. Executes the HEGO monitor. EVAP 6. Cruise at 72 to 104 Km/h (45 to 65 MPH) for 10 minutes (avoid sharp turns and hills) Note, to initiate the monitor: TP MODE should =PT, EVAPDC must be >75%, and FLI must be between 15 and 85% Executes the EVAP Monitor (If IAT is within 4.4 to 37.8° (40 to 100°F)) Catalyst 7. Drive in stop and go traffic conditions. Include five different constant cruise speeds, ranging from 40 to 72 Km/h (25 to 45 MPH) over a 10 minute period. Executes the Catalyst Monitor. EGR 8. From a stop, accelerate to 72 Km/h (45 MPH) at 1/2 to 3/4 throttle. Repeat 3 times. Executes the EGR Monitor. SEC AIR/CCM (Engine) 9. Bring the vehicle to a stop. Idle with transmission in drive (neutral for M/T) for 2 minutes. Executes the ISC portion of the CCM. CCM (Trans) 10. For M/T, accelerate from 0 to 80 Km/h (o to 50 MPH), continue to step 11. For A/T, from a stop and in overdrive, moderately accelerate to 80 Km/h (50 MPH) and cruise for at least 15 seconds. Stop vehicle and repeat without overdrive to 64 Km/h (40 MPH) cruising for at least 30 seconds. While at 64 Km/h (40 MPH) , activate overdrive and accelerate to 80 Km/h (50 MPH) and cruise for at least 15 seconds. Stop for at least 20 seconds and repeat step 10 five times. Executes the transmission portion of the CCM. Misfire & Fuel Monitors 11. From a stop, accelerate to 104 Km/h (65 MPH). Decelerate at closed throttle until 64 Km/h (40 MPH) (no brakes). Repeat this 3 times. Allows learning for the misfire monitor. Readiness Check 12. Access the ON-Board System Readiness (OBDII monitor status) function on the scan tool. Determine whether all non-continuous monitors have completed. If not, go to step 13. Determines if any monitor has not completed. Pending Code Check and Evap Monitor "Bypass" Check 13. With the scan tool, check for pending codes. Conduct normal repair procedures for any pending code concern. Otherwise, rerun any incomplete monitor.
Note: if the EVAP monitor is not complete AND IAT was out of the 4.4 to 37.8° C (40 to 100° F) temperature range in step #4, or the altitude is over 2438 m. (8000 ft.), the Evap "bypass" procedure must be followed.Proceed to step 14. Determines if a pending code is preventing the clearing of P1000. Evap Monitor "Bypass" 14. Park vehicle for a minimum of 8 hours. Repeat steps 2 through 12. DO NOT REPEAT STEP 1. Allow the "bypass" counter to increment to two.
© Ford Motor Company

If the engine has a rough idle you know you have a miss-fire or other problem with one or more cylinders.
When you shift into overdrive the engine is working harder than in normal drive because of the lower torque/RPM.
So any slight miss under normal conditions will be magnified in overdrive or with the ac on.
See if you can nail down the cause for the rough idle.

Possible Idle air control, simple to change on the throttle body

you can't clean a egr , been tried by many, works for temporary solution only, best place to start

Sometimes a rough idle like that is a fuel filter. As you've already done the plugs and wires the fuel filter would be my next bet.

Could be throttle position sensor. Does it run rough at 20 mph or smooth?

Try this relearn procedure hopefully it will help

Vehicles equipped with engine or transmission computers may require a relearn procedure after the vehicle battery is disconnected. Many vehicle computers memorize and store vehicle operation patterns for optimum driveability and performance. When the vehicle battery is disconnected, this memory is lost. The computer will use default data until new data from each key start is stored. As the computer memorizes vehicle operation for each new key start, driveability is restored. Vehicle computers may memorize vehicles operation patterns for 40 or more key starts. Customers often complain of driveability problems during the relearn stage because the vehicle acts differently then before being serviced. Depending on the type of vehicle and how it is equipped, the following complaints (driveability problems) may exist:

Harsh Or Poor Shift Quality
Rough Or Unstable Idle
Hesitation Or Stumble
Rich Or Lean Running
Poor Fuel Mileage

These symptoms and complaints should disappear after a number of drive cycles have been memorized. To reduce the possibility of complaints, after any service which requires battery power to be disconnected, vehicle should be road tested.

Vehicle Preparation

Ensure all components are connected. Ensure transmission fluid level is correct. Warm engine to normal operating temperature. If vehicle has been repaired, perform KOEO and Continuous Memory Code Self-Test and ensure fault codes are not present.

Computer Relearn Procedures

Idle Relearn Procedure

Place automatic transmission in Park or manual transmission in Neutral position. Ensure the emergency brake has been set and all accessories are turned off. Start engine and bring to normal operating temperature. Allow manual transmission vehicle to idle in Neutral for one minute. Allow automatic transmission to idle in Neutral for one minute and then to idle in Drive for one minute. Once initial relearn is complete, process will be completed during normal driving. Always complete the procedure before returning the vehicle to the customer.

Drive Cycle Test (AOD-E, AXOD & AXOD-E TRANSAXLES)

With transmission gear selector in Overdrive, moderately accelerate vehicle to 50 MPH for a minimum of 15 seconds. Transmission should be in 4th gear. While holding speed steady, lightly apply and release brake for about 5 seconds. Stop and park vehicle for a minimum of 20 seconds with transmission gear selector in Drive. Repeat procedure 5 times. Always complete the procedure before returning the vehicle to the customer.

Drive Cycle Test (E4OD)

With transmission gear selector in Drive, press Overdrive Cancel Switch (LED should light). Moderately accelerate vehicle to 40 MPH for a minimum of 15 seconds (30 seconds above 4000-ft. elevation) Transmission should be in 3rd gear. While holding speed steady, press Overdrive Cancel Switch (LED should go off) and accelerate from 40 MPH to 50 MPH. Transmission should shift from 3rd gear to 4th gear. Hold speed steady for 15 seconds. While holding speed steady, lightly apply and release brakes enough to turn brake lights on. Maintain 50 MPH for about 5 seconds. Stop vehicle for a minimum of 20 seconds with transmission gear selector in Drive. Repeat procedure 5 times. Always complete the procedure before returning the vehicle to the customer.

Not saying this for sure, but I had the same problem, and i have a 1994 xr7 V6 3.8 L , and all u need to do is set the idle down manually because your computer could have seen that the injector was stuck open, and tried to turn up idle to keep up with the amount of fuel being pumped, worth a shot :P

you will have to read the diagnostic code that the computer is sendig for the check engine light to activate