When a trans swap is done, the wiring to the wheel sensors is moved and unclipped from the subframe etc. While it sucks, I'd check over the wiring down at the subframe where the speed sensor wiring is connected to the main harness and lays around the frame. The driverside is pretty clear of issues when doing the trans, the passenger side can get caught up on the engine mount and possibly pinched.

If I were trying to hunt it down..that's where I'd start.