Never heard of killing a TB by actuating the blades manually. I've sat around while my car was in pieces just dickin with the T-body blades. Usually I clean the T-body any time I've had it off the car, which is quite a few times, and when I clean it I get after it with the same CRC MAF cleaner and a toothbrush, pushing the blades open and cleaning around the blade shaft. I've never had issues with my T-body other than replacing a TPS once. You probably could damage the gearing if you were rough enough about it, or fighting the motor while it was online. But moving the blades while the T-body is unpowered will damage it? GTFO and leave the crack pipe behind. Someone lied to you.
OP, any harness or wire you touched needs to be closely inspected. Particularly any harnesses that you removed, such as MAF and TPS/Motor harness. Make sure you look at the pin side and make sure no pins both at the harness and the connector were damaged/bent/loose. Also to verify the TB is actuating properly, as stated above you'll need a helper to turn the car to "on" without starting. While you look at the throttle blades, no intake tube, just exposed. If the T-body opens and shuts, it's prepped for startup. With the key "on" you should have them push the gas pedal slowly, and make sure the throttle blades open accordingly. If all of that works, you need to either sit down with a meter and test your TPS sensor, or just replace it. When having sluggish throttle or bad throttle response, along with other throttle errors, it's a 50/50 bet as to it being a dirty throttle body or a failing/failed TPS sensor. I've never had issues with the T-body being dirty, but I have had to replace the TPS sensor before. It randomly would throw the wrench light at me, I'd shut the car down and restart and it would go away. Days later, it would throw the wrench again. Replaced the TPS and never had a wrench light again. Though I didn't notice bad throttle response before the wrench light.
If you go through the wiring, checking the T-body, checking the TPS, the only other place to look would be the gears. OEM gears don't have a reputation for being faulty, but it could be possible. There is a procedure to servicing them and keeping them clean, but it's important to inspect the gears to make sure none have stripped, in your case. I could see if a gear had stripped a portion of its teeth in the right spot would give you the issues you're describing.
