hi! i just wanted to add our experiences w/ microchipping. our vet in minnesota uses avid. both our kitties were chipped before our move to san diego. our vet here uses home again. when we brought playdoh (our kitty) in for her annual exam, we told her new doctor she was chipped w/ avid. we didn't have her number w/ us to give him. he said it didn't matter which company her chip came from, the wands work w/ all. he then scanned her & wrote her number on her chart~ remember he uses home again.
as for your concern w/ the pain, it's the same as getting a shot. our kitties are ok w/ shots, cali (our yorkie) cries a little. both our kitties were done super quick! they were a little sore in the area of injection, but otherwise acted the same.
another thing to consider, we had cali microchipped when she was spayed. so she definitely didn't feel it. i don't know what your plans are for your baby, just another option for ya.
i hope this helps! good luck w/ your decision!