It's been a few weeks since the last post, but I have checked all of the vacuum lines and found no problems. If were to be a vacuum line wouldn't it cause the engine to rev higher rather than studder and hesitate. The only two things I have left to do, before I start dumping big money, is to replace fuel filter and possibly the coil. I raised the idle on the truck which aided the hesitation but its still there. That in my eyes rules out a fuel issue. I was thinking that maybe the coil is going bad and at lower rpms it causes the engine to miss because of low voltage? Anyone with a similar problem find any fixes?
There is not adjustment to the idle on the throttle body, the adjustment you have mentioned and adjusted is the adjustment to your throttle body blade to keep it flushed and seated properly on the throttle body bore. Adjusting that will cause you to have more issues then should have.
The IAC (Idle air control) valve regulates the idle if the engine and will cause issues if it's dirty with carbon build up, also a carbon up EGR valve will also cause this along with a bad vacuum line.
When you adjusted the throttle body blade, the TPS will indicate to the PCM that it's open and will not send the proper signals to the IAC since the PCM thinks your on your throttle. So any adjustment to the engine's Idle make from the PCM will not be made and your idle will be random on engine load, air temperature, ECT. The throttle blade should be closed 100% without any binding to your throttle body bore.
Try this to reset your IAC and PCM. Turn your ignition keys to the run position "engine not running" then pull the fuse out for your ECM, think there are two of them so pull them both and after 2 min reinstall the fuse. You should hear the fuel pump energize the fuel line.
Now to reset the IAC turn the ignition off for 1 min and then turn your ignition to the run position for 30 seconds then start the engine. The 30 seconds will reset the IAC, you engine may stall at first but don't touch anything and let it stall out.
Turn the ignition off again for 10 seconds and turn the ignition to the on position again for30 seconds and start the engine. Your engine should rev 1000+ and drop after a few seconds when the engine reaches operation temperature, then go for a test drive for your PCM to relearn your engine and transmission sensors. So you may find your transmission to shift firmer at first but then the PCM will compensate for it and bring it back to factory condition.
Good luck and keep us posted and back the throttle blade adjustment back to where is should be.