Yes, if someone has noticeable symptoms during the initial outbreak, it will occur within a couple weeks of the sexual encounter of the exposure. However, a significant number of people with genital herpes will not have noticeable symptoms during the initial outbreak. In fact, when blood tests are done in studies to determine the prevalence of antibodies to HSV2 in the population, about half of the people do not recall any time when they previously had any sores. So the fact that there has been months since the last sexual contact does not exclude the possibility of herpes.
I would also note that a condom only offers limited protection against herpes transmission, or any STD that is transmitted by skin-to-skin contact. Since the condom does not cover the entire genital skin, there is still ample opportunity for skin to contact skin and allow for transmission. In studies looking at couples in which only one person is infected, condom can reduce the risk of transmission by about 50-60%, but it certainly is not complete protection.
A herpes sore will usually start as a bump and then progress to an ulcer, and that would not be due to the application of apple cider vinegar.
Yes, it is possible that an ulcer of the genital skin could be an aphthous ulcer, although it is less common on the genital skin than in the mouth being confused for oral herpes. Statistically, we see more genital ulcers from herpes than from aphthous ulcers. But this is part of the differentiation that would need to be done by your doctor.