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That doesn't necessarily mean they were in the correct order to begin with though, I've learned never to take anything for granted. I'm sure you've checked this...
Just out of curiosity, how was the truck running before you did all this work to it? Perhaps a little more history on your rig will help us help you better.
So all the obvious stuff has been covered. If you have good fuel pressure, good ignition, and your transmission is functioning normal, that just leaves all the sensors in the intake manifold and elsewhere that the computer uses for tuning. Have you replaced the MAP sensor, TPS, coolant temp sensor, IAT sensor, and o2 sensor?
everything was fine untill the tranny went.. then after that my truck has been running bad...
Well...that's not exactly the history I was looking for but, it seems to me that the problem may still be the transmission. Was it a rebuild, salvage yard trans, was it the right trans for the truck? Give us a bone here man, we're tryin' to help but getting information from you is like pulling teeth...LOL