hi ram, i would either buy a honda service manual or download it, so you can see how much work is involved. if you're not comfortable doing the work yourself, then you can get estimates from the shop or other shops on rebuilding or swapping. i would assume that the shop you brought your bike to should have already gave you an estimate and parts list on rebuilding? i think it's going to be expensive either way because paying someone else to do the work gets pricey.
when you rebuild a motor, you will know the parts are replaced with new parts, when swapping a motor, you don't know. i think you should get a couple estimates and then you can weigh your options. hope that helps