Brief Update: I had my PCM flashed. He confirmed that the rear tire size was off by quite a bit, but he still couldn't fix the transmission stack shifting issue. He put my truck on the dyno and the transmission shifted perfect, but when he drive it, it did its usual act. This guy specializes in custom everything and building race cars. He knocked a nice chunk off the bill because he couldn't figure out what was going on with the transmission issue.

Basically, at a stop, if I floor it, it shifts perfect through the gears. If I accelerate normally, then it stack shifts pretty early, and when I floor it then, it doesn't downshift and pick-up and go - it just gradually accelerates. Would the vss signal cause an issue like this if it's not giving the right signals. The dyno did determine that my truck speedometer is five miles slower than it actually says, and my speedo is reading from the transfer case. I'm still not sure what to try. It would be really nice if i can get the transmission to work properly.