Max wasn't quite as skittish after his amputation, but he was definitely sensitive about it. For that matter, so were we. My wife and I tried to avoid petting him in that area because we were afraid of accidentally touching it and causing a yelp or tearing a suture.

Concentrate on other areas that aren't near the site, wherever she loves being scratched (Max always loved the sides of his head and his butt). Give Milkshake lots of attention in those areas so she stays used to physical contact and attention. Don't try sneaking any occasional pets in near the area; just get her comfortable with being petted elsewhere. Max was sensitive for about a month after his amputation, so don't expect quick results. The big victory for us was when he started laying down on his left side again (he lost his left front leg). That's when we knew the nerve endings that led to his lost leg had finally died off and he was comfortable again.

So keep your eye on Milkshake and take your cues from her. Once she starts ignoring that area (and eventually she will), it's safe for you to try petting her there again… slowly, though. She'll get there; just be patient and give it time.

I didn't know Max when he lost his leg, but I agree with lots of treats.  I used to have a greyhound and to get her to let me cut her nails, I'd smear peanut butter all over my arm and let her lick it as I clipped.

Also, for my patients (human amputees) I always suggeste desensitization with a variety of textures--hand, a towel, newspaper.  They all have different feels and some may be less tolerable than others.