I just went through the same thing. I had to use a Fannie Mae approved contractor though, but FHA standards were used when appraising the home. The appraisal came back contingent to repairs on June 11. The repairs were not complete until June 29 (and they were minor!) Then it had to go back to underwriting and we just made it back out. Throughout my entire process, I have had 7 extensions. (The sellers would only give 1 week at a time each time.) In my contract, I had to pay $7 for two days if I had any extensions. (Strange, right?) But I didn't have to pay anything past day 2. Give your contract a good read to make sure because all contracts are different. Best of luck.
I don't know if this will make you feel better or worse, but I've been purchasing my home with USDA since the beginning of April and I don't close until Friday. It's a looonggggg journey.