Rashes in the perineum (that's the part of the skin you're talking about) are usually irritated rather than ifected with yeast or fungus. The chronic, intermittent nature of your problem alos argue for irritation. Perhaps diarrhea started or aggravated the process.
I doubt any kind of STD. (I'm not sure what you mean by: "I have been checked for the usual STD's, and have not been diagnosed." Diagnosed as not having STD, or not having any diagnosis?)
Needless to say, it won't heal if you don't stop scratching. I would use a heavy moisturizer like vaseline leberally and often. I would also suggest an over-the-counter itching lotion like Prax, Sarna, or Benadryl. Use one of these every time you feel like scratching--it will take the itch sensation away. Hydrocortisone from time to time may help too.
I recommend a visit to a skin doctor, at a time when you haven't been scratching, to get a definitive diagnosis and perhaps other suggestions.
Best.
Dr. Rockoff