it sounds like you have a new motor and rather than take it out as an assembly you have unscrewed the four torx bolts that hold the motor cover on? This would not be a motor swap.... the window motor is teh entire assembly. Some refer to the half of the assembly that has the drive gear as the "regulator", and that is incorrect. The regulator is the metal scissors assembly that lifts the window.
If you are trying to swap a window motor, I really recommend that you take your time and swap the entire assembly. Yes, the original motor is riveted to the door frame, and yes it is a pain in the rear.
When I did mine, I removed the window glass to prevent breaking it. Not as hard as it seems if you have a good toolset and the Bentley manual. Next, the rivets holding the regulator and motot were drilled out, so that the entire assembly could be removed and then the motor un-bolted from the regulator. This is a good time to buy and replace those plastic clips that slide in the track and hold the regulator to the window track. Also, this is a good time to completely clean everything (regulator and tracks) and lubricate the tracks and regulator. The track that holds teh rear portion of teh window actually comes out also, so why not remove it so you can clean and lubricate it like new?
Before assembly, I would bolt the motor to the regulator and operate the motor to make sure it works correctly. It sounds like the rear half of the motor was removed, and if put back on incorrectly the motor will nto spin in the correct direction and therefore won't work.
Upon assembly, you will need to buy nuts & bolts to replace the rivets which you previously you drilled out.
Also, this is a good time to renew the plastic clips that hold the door panel trim to the door.
If you take your time and do everythign right, you will end up with a window that works properly for a very long time -- including one-touch operation. Every piece of dirt, sand, grit, and rust needs to be cleaned out of all moving parts as well as the original grease from the factory. All moving parts need to be greased with new grease, like lubricating grease -- not a silicone liquid or WD40.