That's ALL you were doing/did, removed the secondaries?
You need to back-track your steps because something is unplugged.
Think about it this way .... you just took metal plates off a moving throttle bar, the bikes computer doesn't have a clue that they are missing right? There is no way that it can .... unless .... something in the area was knocked/left loose or came unplugged.
ALL your plate screws are accounted for?
The throttle bar isn't stuck/jammed for some reason? (it needs to still be moving when the bike is on) You can check that visually by observing it from the outside (if everything is assembled) or inside (if the air plenum is still off the bike) and cycling the ignition. If it is not moving at all, the stepper motor is unplugged.
Not having the temp sensor properly plugged in will set an engine light but it wouldn't run poorly as you described. A LARGE vacuum leak can make it run bad, but may not set off the light right away.
Check the obvious first and let us know if you found anything. I'll get the book out and see if there are more possible causes.