Do what Kyle said and press the coupler off the shaft... that is the proper way to do it.
If the puller you used bent the flange of the coupler, or if you have serious (measurable) wear on the shaft, then consider replacing the whole thing with a dual taper ARE.
Hopefully the tranny rebuild works out for you. Most people end up goofing something up (there seem to be a few tricks not covered in the manual) and end up pulling the trans a second time for a professional rebuild. That should only cost in the $700-800 range, so that $1200 quote you got is way out of bed.