Hi @Eric Oswald
I have never had much luck with the habitat for humanity thing. I've found that I wasted too much time driving between them only to find sets of cabinets that were missing something or special order items that rarely worked for me. I did score a case of 30 or so brand new doorknobs for next to nothing, so that was cool.
Here are my suggestions:
Countertops: Imperial Design in Gloucester City. They were priced right and very quick. Excellent quality. I've only gotten formica from them, but I'm sure they do just as great a job with granite.
Appliances: If you want a package I have always found Home Depot/Lowes had the best package pricing. If you need a piece here and there you can usually pick up something in the clearance section there for dirt cheap.
Flooring: Again, I've use home depot/lowes. I have them install carpet but always did the hardwood/tile/laminate install myself.
HVAC equipment: I used ACE plumbing in Vineland to buy the material. You get the 3.5% sales tax rate there. I also picked up tankless water heaters from them.
As far as contractor, I have one that I used but he is not the cheapest. I have gone the route of cheap contractor and paid for it in the end. I can send you the name of the contractor if you would like. They are located in Williamstown and always show up and do great work.
Let me know if there is anything else that you need and I can pass along my contacts.
Good Luck!
