Thanks for the replies, everyone.
I'm not getting a CEL. Might be because I'm not getting much of anything as far as lights go...
As far as I was able to research, the gear ratio for 5MT transmissions was the same for all non-turbo US-made Legacies between 90-96 (the new trans came out of a 94).
I didn't unplug the engine harness except where it connects to the transmission (one connector, right on top of the trans, the one that now has no ground wire)
The battery cable grounding wire is connected and tight... (both the one to the frame and the one on top of the bell housing)
Would a speed sensor screw with it this much? I kept the speed sensor that came with the new trans because it looks like my speedo cable plugs into it just fine, but I still have the old sensor...maybe I should swap them? Can't think why that would give me starting problems, though...
Could it have to do with the starter motor? As far as I can tell all electrical connectors/grounds on the starter are good, too, and the starter itself is part of a rebuilt engine that was JUST put into the car, so unless something happened to it sitting out while I swapped the transmission, it's a good one...
Again, thanks for the replies. I will see if I can flash any kind of CE code, even though the light's not coming on.