There's a lot of stuff in this manual, and how to test the circuits for the shifter. It's called the interlock system. There is an interlock control unit, key interlock switch, shift lock solenoid, and other shit. Did you just swap the TCU, or did you mess around with other stuff at the same time? Like I mentioned earlier, I've had weird stuff happen. I pulled the ECU fuse with the power on once(duh), because I was in a hurry, and my door locks stopped working. I reset everything and they worked again. Recently, I had about the same thing you guys are experiencing happen to me, while installing my alarm. I bumped a relay or something around the interior fuse box of the car. I was using the key to get into gear until I pushed on all my fuses and pressed my harnesses together better. Double check your connections, I'm willing to bet you'll be amazed how simple the answer is. If not, look up shifter interlock system.(93 HONDA SHOP manual, for prelude, 23-161)
My local Honda parts guy is cool as fuck, and is more than happy to let me flip through his four inch thick books.