There has to be a wire that just isn't connected properly. What I might do is take the door panel off of the other door, and makes sure both sides match up wire-to-wire. Examine the on that works to fix the one that doesn't. Sometimes it takes that to figure it out.

I did a power window swap on my Si. It took me an hour to realize the switch to not allow the passenger side window to roll down was pressed and was the only reason my window wasn't working