So I'm driving down the road, and my LH rear window falls into the
door.

I take the panel off, and the power window regulator is broken.
The plastic guide at the top of the assembly has snapped, freeing the
cable.
The motor also burned up.

I got a new regulator and motor, and installed them inside the door.
The window now rolls up almost all the way, but stops about an inch
short of being rolled up entirely.

So I disconnected the window from the regulator, and pushed the window
into the up position myself.
It was surprisingly hard to do this.
Then I rolled the regulator up, hoping that if I connect the two in
the up position, it would solve my partially-rolled-up problem.

However, the regulator shuttle and the window's connection mounts are
horizontally misaligned in the up position by about 1 centimeter.  So
I can't connect the window to the regulator shuttle in the up
position.

I compared the old regulator with the new regulator, and they are
virtually identical.

Is it common to have this type of alignment problem when installing a
new regulator?