I took a video of the bogging down that I'm getting. The vehicle was in park, warmed up fully with no check engine lights. I used my OBD-II USB scanner with ScanXL and it turned up no "hidden" check engine faults.
If I slowly accelerate the engine to, perhaps 4000, there'* no problem. If I step on the gas abruptly, I get a stumble from the engine (as you hopefully can hear in the video).
With the transmission shudder, If I keep my RPMs below 2000 or so, I can prevent the shudder from happening, but even in 2nd gear, The car will shudder under heavy throttle. It seems like temperature has an impact on this. I just drove the car after it was sitting here (about 40 degrees) for a few hours. I took off right away and even under full throttle, I didn't get any hesitation.
I filled up with 89 octane and threw in a bottle of fuel injector cleaner for good measure. I'm thinking this is an ignition problem or sensor (perhaps MAP, TPS, or MAF?) Using ScanXL and getting the GM PCM data stream, the TPS was giving various readings from negative degrees to about 30 degrees, all when the car was idling. I can post some of the data if that would help...