I think if the clinician looking at it thought it was likely folliculitis, then it likely is. That is what it sounds like from your description, actually as well as the fact that it was near a shaving time. No, the primary outbreak is not normally on the scrotum or look like a paper cut. The first outbreak, if symptomatic, is different than that, both in location and appearance.
If your partner has neither HSV 1 nor HSV 2, this would likely not be a primary infection unless she has not had time yet to seroconvert, based on the dates of her last experience prior to you.
I think 5 days is pretty far out to swab, yes. I think you should finish the doxycycline.
Also, the fishy odor is likely either trich or bacterial vaginosis. Was she checked for those?
Terri