1) If the most recent test was performed as a paired test instead of an individual test, what would the results have looked like/would it have made a difference in the test or results considering the negative result?
No, except it is possible that they would have called the indeterminate a negative on the second reading.
2) I was taking isotretinoin (accutane) for facial acne during the time when the indeterminate HSV2 result occurred. Could this medication have had an affect on the western blot result?
3) Recently, and after the completion of the isotertinoin treatment, I have started to develop some what i believe are pimples (not clusters, only individual spots) on my butt checks only. Can HSV-2 present itself as single points on the buttocks area, or is this more likely pimples/acne?
Rarely. Usually lesions on the buttocks come in groups.
I thank you seriously need to stop doing this testing.