Yeah i use to actually change those motors on the side actually... Unfortunately I work and go to school 7 days a week in January... and I have state Finals in February...

I'd look up window motor install.. or Shoebox's website on installation...
Once you've done them a couple dozen times its a 45 minute job. But the 1st time can be a couple hours because you cant see really what your working on.. Those "tracks" that you say is scratching your window have Felt covers on them.. when that felt comes off its metal which is probably scratching your window. You'll see when you take your door off.... you have 3 rivets that hold in your motor... Do not drill out the railing that connects the window rail to the fiberglass door. You have to feel for the rivets that hold the window motor to the rail. then drill through the fiber glass to reach the rivet.. Remove your front speaker too...