I guess my puppy isn't really a puppy anymore. From what I've read she is at least 6 mo. Old. Getting her fixed was definitely on my list of things to do and in my puppy budget but, her start was a rough one (parvo) and we were only guessing at her age. Now she's in heat. She's had only her first set of puppy shots. My question is can they spay her? Do her shots need to be readjusted to fit her newly guessed age? Ill call her vet (im feeling a bit better about him now) in a few hours and ask again but, at the moment id really like a little insight if anyone knows.

The shots should continue on as they would even if she started at 6 or 8 weeks.
First set, then 3-4 weeks second set, 3-4 weeks then the third set.
It's the timing that is important with vaccines.
Rabies is the only one required by law, not sure about where you are but I think the 16 week rule is nationwide.
As far as spaying her while in heat, it is perfectly safe, but the reproductive organs may be swollen, the incision may need to be a little larger, and can be a little messier for the surgeon to perform, there may also be an "in heat" charge added to her bill, so it's worth asking beforehand if that is the case at your vets' office.
Most surgeons will spay an in heat animal without batting an eye.
She got a rough start but it sounds like she is coming along just fine, good job Mom.
Different vets have different preferences yours may not want to spay until she has another set of vaccines, but given her history I'd let him make that call.