WTF? When you said the gear indicator was stuck in N, I thought it sounded like a TRE was installed. That would be normal because the reason to use a TRE is to lock the bike in the N fuel map. ...but the rest of it is totally weird.
Sounds like they had a busy day at the shop. I'd ask them what connectors they unhooked and check those myself but I wouldn't be real keen on sending the bike back to them before I checked the easy stuff myself.
There is a connector (4 in all) to each injector on the T body assy. Also a connector that goes to the 4 stick coils. The main wiring harness would have also been disconnected to take out the T-bodies and that is one one of the biggest bitches to do when you work on this bike. There could have easily been a wire damaged on that. It's easy to check that it is connected though. Press the connectors together firmly and it will click if it was not fully connected. Check the crankshaft sensor connector too. Just check everything you can without having to remove the Tbody assy (hopefully). You might find this useful.
I'd also check the coolant drainplug too and the clamp screws on the top and bottom of the T-body bores.
* Last updated by: Rook on 5/30/2014 @ 8:00 AM *
'08 MIDNIGHT SAPPHIRE BLUE Now Deceased