Well for the first time since I have owned the car, WOT shifts were ok when warmed up. Normally the entire car would shudder, and jerk. I had been playing with things and been disconnecting things to see if there was any change. I disconnected the MAF and no change. I tried putting the gear selector in 1, and holding the RPMS at 4500, and then selecting 2 so it would shift there with mild throttle, and the shift was perfect. But as soon as you put it in drive, and accelerate rapidly; it shifts very firm, and jerks into the next gear. Finally I disconnected the EGR. AT first it did nothing, but within five miles the shifts got better. It did not shift as hard into the next gear. Finally I went WOT, and the shift from 1st to 2nd produced no shudder, or shimmy. There was still a firm jerk into the next gear under normal driving circumstances, but the WOT shift was perfect... could the EGR valve be causing all my issues? I am just lost here, everything else seems to be testing out good, but it still would shift horribly but it still does not have the P1811. So I am lost with this.

You may want to go to a transmission shop and have them take a look.

You might want to consider doing the basic shift kit and conversion to DEXRON VI. I had a very simular problem to your, did the shift kit and DEXRON VI conversion, and tranny is doing well 60k miles later. I think you may be surprised at the outcome of this procedure.