Something isn't right in there. There really isn't any way to move that pulley that far in unless someone beat it with a hammer or something. Everything should line up just fine if that was a complete motor you bought. Are you sure that the cams are in the right location in the bearing mounts in the head?
I wouldn't try to use a puller to get the WP into the right location. Proper way would be to support the pulley all around and press the shaft down. I'd have a machine shop probably look at this one. If you bend the pulley at all with a regular 3 jaw puller (which would be extremely easy) your belt will not lost very long and shred itself repeatedly from the pulley being out of whack.
HTH and sorry for the bad diagnosis,
Rick
