I have one more piece of diagnostics to try that may at least narrow down the problem. As you can tell, I am sharing a lot of frustration, and can't get a grasp on it.
If I am correct, you had at one time mentioned that you added a power commander and a tune on this bike, and noted that it ran fine.
Well, is it possible the sensors are bad on the Autotune? Before anything, I would try the following before tearing into it again. Disable the sensors, and set the AFR's in override? for 12.5 or richer across the board and take it for a ride. If i am not mistaken, disabling the closed loop from the module may do this, but I cant read enough to go over that detail. Perhaps this process of elimination will help, and at least feed the motor the extra fuel.
At least you could discover if the AFR metering side is actual hampering the flow inadvertantly. A 02 sensor can go bad, or, it can get coated, and send erroneous signals to the TMAX.
Rhino
Rhino, if you disable the sensors (basically taking it out of AutoTune Mode) then the AFR Override isn't an option.
Don, I'm surprised nobody has recommended this yet, but I did it on mine, while it didn't help me any, it might you. Get the bike good and heated up, then with the Laptop connected, (you are using a laptop I hope cause this won't work with a desktop, atleast not without a really long extension cord), setup the monitoring function and save it to a file, then go for a ride with the laptop in your tourpak, create whats happening and then go back and playback the file, it takes a while cause the playback is viewing something like 8 samples/second, also this information may help Zippers determine your problem (assuming they can) if you send them the file. Ya gotta really pay attention during the playback but after looking at it for a bit you can see where you shift and accel and blah blah blah, it'll all make sense before long. Just make sure you turn on monitoring for major functions like AFR, Timing, TP........anything you think might be helpful.