If you had to remove the MAF during the install, then pull it back out and make sure its facing the right direction. Otherwise, I would be led to think you may have damaged/pinched a wiring harness during the trans removal and/or trans install.
Also, check your main engine ground wiring. I just remembered a Jeep Wrangler I helped a buddy do a lift and clutch replacement on and during the trans removal, we somehow damaged that main ground wire, which caused the wrench light to come on. The lighting wouldn't work correctly either and the blower motor burned up, but yours may not be damaged as badly.