The passenger side power window is sort of a slave switch/system. The circuit goes through the driver's side door before heading on over to the passenger side, but the manual door you just installed doesn't even have that harness, so what do you do?
Basically, (and this is assuming you don't swap over all your power window stuff to your other door) you need to cut the harness off the door you took off, and solder the wires together (and then protect from shorting) like this:
Plug that back into your vacant harness connection under the dash, and your passenger side window should work again.
I realize this is a very specific situation, but believe me, its sort of a b**** trying to figure it out if you ever have to do it (the wiring diagrams are a bit cryptic). Hopefully this will save someone some headaches.