The secondary removal in conjunction with the GiPro improves the throttle response. The GiPro will still improve the power in 1st-3rd, you just won't have the snappy reaction from throttle inputs. Still, there has to be some way of taking care of your problem without reinstalling the plates. No one else seems to have had the same problem you are having with the check engine light and codes. I was thinking that if the primary TPS rod is adjustable, then wouldn't the secondary one be adjustable as well? If it's just a matter of the rod turning too far that is setting the code, what about just adjusting it so that it doesn't set a code? The whole rod and plate thing is serving no other purpose since the plates are gone, so it wouldn't hurt anything to adjust the linkage to adjust the rod right?
I think I'd start there rather than reinstalling the plates. Do you have any way of resetting the code, like an OBDII interrogator? If nothing else, I'd adjust the linkage so the rod doesn't turn so far, reset the code and see if it sets again. If it does, keep adjusting the linkage shorter and resetting the code till it stops. Getting into the ECM with TuneECU or Tuneboy would allow you to read the TPS values, but I don't see how that will help since the values are probably right and it's just the linkage turning the rod too far?
I don't know for sure what to tell you to do to fix this, I didn't have the problem occur when I removed them. My suggestions are just that, suggestions from me trying to picture the problem in my head. Hopefully there will be others with more ideas come along here.
I was also thinking ... if the TPS was using the plates as a stop and removing them has allowed the rod to over rotate ... what is supposed to be the stop? Making adjustments so that the rod stops rotating where it's supposed to stop should fix the problem. Sound right to you?