The lesions that you describe is not likely to be herpes. Typically herpes infections last a few days (up to 21 for first episodes), not 6 months. As you point out, when they occur they tend to have small blisters which then break to form shallow ulcers before they heal. What you describe does not sound at all like herpes.
As far as your tests are concerned, IgM tests are not recommended for herpes diagnosis as they are often falsely positive due to detection of other antibodies from other past infections (like chicken pox). I know of NO expert who recommends IgM testing for herpes and there is general consensus that IgM tests are worthless. In addition, given the duration of your lesions, if you had HSV, an IgM test would likely have been positive. Finally, had this been herpes, your lesions should have improved and then healed with antiviral therapy. Thus to summarize, there is nothing of what you report that suggests that you have herpes. As for your specific questions:
1. Yes herpes lesions can sometimes have an atypical appearance but they still tend to be self limited and not last 6 months. Your lesions do not sound like herpes.
2. See above. I would urge you to ignore the IgM test result. It is not a good or particularly useful test. I have NEVER recommended its use.
3. Treating something that is not HSV as herpes will not help. I agree with GYN no. 2 that this sounds more like a dermatitis than HSV. If it is not getting better, I'd suggest a dermatologist.
4. I sincerely doubt that this is an STD and doubt that there is any reason to abstain from sex.
Hope these comments help. EWH