the pits refer to the pit they make u drive over for an under vehicle inspection.
As far as getting it sorted, your pretty much in a self dug hole. Your lucky you got so far with the car yard.
Buying a modded car to start u knew that it wasnt std, so u shouldve taken it on the chin and gone to regency and got it off defect. It wouldve costed a little, but im sure if u took it to Shaun @ Boostworx to get it back to std he wouldnt leave the car running like sheit.
All i can suggest is if the car is running, and std, take it through regency. If it doeesnt pass, get the problems fixed until its off.
Then go see Shaun @ boostworx, and tell him the problems about the car and see what he says. You will have to spend a bit of money now to get it running and on the road. I think u have cut all ties with the caryard now anyway so dont bother going back...