To summarize your situation as I understand it, the questions are, what are these bumps? and what should/can be done about them. I hope that my comments will be some help but really, now that they have come and gone as well as not responded particularly well to Aldara, the right thing to do is to have them looked at by a dermatologist. Your regular doctors should not feel bad about this - they have already acknowledged that they don't know what they are due to, thus they will learn something too. Beyond that, there are several other comments which may be helpful as well, at the end, my impression:
1. The "vinegar test" is notoriously unreliable. Only about half of what turns white are warts and some warts are missed by it.
2. Vinegar is unlikely to be effective in treating warts. While vinegar is essentially dilute acetic acid and acetic acid is used to treat some warts, the concentration of acetic acid in vinegar is too low to be effective for warts.
3. I take it that most of your lesions are now on the scrotum. Warts on the scrotum are rather uncommon while other, non-STD processes such as folliculitis, benign cysts, and skin tags are all relatively common.
My guess is that the bumps you have noted are not warts or any other STD but some other benign process. As to which one, there is no substitute to having them looked at by someone who looks at rashes all the time - a dermatologist. In turn, depending on what the dermatologist say, you can get advice on how to manage them, if they even need management at all.
Please let me know what the dermatologist says. Take care. EWH