1) What do you think the likelihood that this is a HSV infection?
Without external genital lesions, I think HSV being the cause of the pain is highly unlikely
2) What are your thoughts on continuing valcyte either to complete a 5 day treatment course or continuing 500 mg daily as prophylactic until my final testing is back?
I would say no as longer courses of antivirals can cause false negatives on herpes antibody tests.
3) If you have gHSV1 urethritis with no lesions, where do you asymptomatically shed from after the acute phase?
The shaft of the penis and possibly anus.
4) What do you think about early IgG testing at 4 weeks?
I would say it could give you a baseline but would not be useful indetermining whether you are infected or not.
I would recommend a prostate evaluation for you.