I had something similar happen to me after transmission removal and replacement, it turned out that the gear cables (in my case reverse) wasn't completely seated in the retaining bracket on the transmission as fooksm described above. Easy to check and fix if it's the culprit; Jack the rear of the car up (use a stand) or use drive up ramps, look up from behind the rear wheel (passenger side) towards the top of the transmission, if one of the shift linkage cables is loose simply press it back into place.
