Just to follow this up:
I got a hold of a service manual for the bike. In the section regarding the subthrottle valve actuator, it states pretty explicitly not to remove it from the throttle body because it is "precision set from the factory". I called a dealer in town and they said they could not reinstall it and that I would need to purchase a new throttle body. This is kind of curious, it doesn't seem like it would be that hard to reinstall this thing with just two bolts on it. If Kawi didn't want it to come off, I'm surprised that it isn't riveted or installed in a way that would make it more obvious that it isn't supposed to come off...whatever.
I also talked to my tuner who does a lot of work with Flash Tune. You can change the values for the subthrottle and secondary TPS, but there is no way to delete it permanently. After extensive discussion about this part and its function, he highly recommended leaving it on and not trying to remove it (or the subthrottle plates). We went over the tables for this part in Flash Tune and the values are pretty interesting and it makes it apparent that this part plays a vital role in the air control to the motor. The secondary plates are never 100% open and are tuned specifically for each gear and rpm. I think it was something like 4th gear at 8,000 rpm at wide open throttle the plates were still only like 65% open. Not only do they control the amount of air being let into the engine but using the angle of the plates, they control the direction that the air is coming in.
If you have enough patience and know how I believe that you can reinstall the actuator on your own. The issue is that the secondary TPS is spring loaded so when you take it off it releases that spring and unwinds approximately 45 degrees. There is no access to it from the backside which makes it difficult to put back on. I managed to do it but it took a minute or two to figure it out. Once you have it back on, if you know the voltage values for different throttle positions you should be able to re-calibrate it by matching those values. I don't know what those values are.
I ended up ordering a used throttle body from a junkyard for like $50 since I had nothing to go off of for voltage values once I had the component reinstalled. I might have played with it a little more, but I'm in a bit of a hurry to get this thing finished by the first race round. I'm actually pretty surprised that this isn't something that Kawasaki can do. If you have the right information, it should be a relatively simple fix. I guess they would rather have you buy a $500 factory part instead of trying to fix the broken one.
