Just recently my truck started bucking and shuddering under acceleration. It got so bad that my SES light came on. It was considerably worse w/ the ac on. It's enough so my overdrive will not engage. Being paranoid, I returned my 1715 tuner back to stock condition, thus erasing the code (so the dealership couldn't read the computer)

So I had them change the plugs, wires, fuel filter, and service the tranny. Getting the truck back it ran like a new truck as the dealer said two plugs were bad and the rest tremendously out of gap. So after a week when the truck gets warm, the overdrive will still not engage and with the ac on I can feel slight bucking, but it's not as bad as it was...Any thoughts on what's causing this. I've thought about the fuel pump, PCV valve...bleh.

99 4.6L 80,000 miles