Thanks for the additional detail, and I hope I can help you here. Please though understand that online I cant state anything with 100% certainty, all I can offer is my best educated guess based on what you've written.
The incubation period refers to the time between exposure to a disease and getting the disease in question. The vast majority of STDs/ STIs have a much longer incubation period than two days, with the exception of gonnorhea, which is 2-7 days. Most of the others are at least seven days.
Two small blisters. If she is thinking about a possible herpes simplex, the incubation there is 5-21 days. So, it is improbable (but not impossible) that these are a new case of herpes; especially as new onset herpes comes with a flu like syndrome very often. Could she have herpes prior to this and not known it? Absolutely. Many women and men have no idea they are infected because their outbreaks are minor. Herpes is one of the most common STDs that Americans have; about 40% test positive for genital herpes.
Other STDS that cause "blisters" or lesions include HPV and syphilis, molluscum, and their incubation period is 10-90 days.
Does your wife shave? Perhaps she has a hair follicle that is ingrown or infected? It is also possible that she may have a UTI, a urinary tract infection. You've been away eight months and may have introduced foreign bacteria to her urethra unintentionally. That would not cause blisters, but it would cause pain on urination and often the area can be sore.
In any event, a sore vagina and blisters are abnormal. I suggest that if she continues to have this pain that she be checked out by her GYN to make sure everything is OK and there is no UTI or anything else. UTIs untreated can cause organ damage.
Here is a link to a page with signs and symptoms of STDs: http://www.fwhc.org/health/std.htm
I hope I was able to help,