Did you replace the entire motor assembly including the cables? I'm in the process of (re)doing my cable replacement only. I believe if you pull on one end, it should unravel the spindle, so make sure that you have the cable pulled out all the way. If you are sure that the spindle is completely unraveled, then I would install ONE of the outside cables (perhaps front) to the door pulley in any arbitrary position (with the pulley on the track). Then pull the other (rear) cable as tight as possible and pull the pulley towards the other end. There are two spring tensioners inside the motor assembly that need to get compressed, and this is done from each side. Pulling the rear cable, it will compress the rear tensioner, and pulling the (already attached) door pulley/cable will compress the front tensioner.
Hopefully this will give you enough room to attach the rear cable stop into the door pulley. When I did my cable replacement, I did it the other way, but it was REALLY tight and I certainly needed to compress the tensioners before I could install the spindle.