I used a condom but it came half way off. 

From the 2 days after the sex I had intense burning of penis and rectum.

1 Week later had a strong sweat and body odor that reeked of ammonia after prescribed a 1g azithromycin tablet.  Friends say I look tired and haggard.

Ignored it but checked the mirror and noticed a small oval hole opening below the rectum that discharges clear mucus sometimes tiny bits of pus and a red ring around the anus that is inflamed. I have to go to the bathroom right after eating it seems too.  Also a small red indent above the rectum.

Penis head glands have Balantitis. I notice extreme pain in groin and scrotum and sharp pain in testicle occasionally. 

The butt crack area is always wet feeling and irritated with burning pain from rectum.

One day after inspecting my penis I rubbed my eye and it has since had a lower eyelid spasm and twitch that wont stop I went to a ophthalmologist who said it was Meibomian gland dysfunction and to do warm compress on it daily to stop it.  

Dry inflamed throat with very bitter salty post nasal drip.

Noticed back of buttox, inner thigh and inner leg burning and itching with wet discharge feeling from rectum that is very sensitive when pants rub near the leg area that it hurts. Lower back hurts a lot right above the butt crack.

Tested negative for syphilis, gonorrhea, chlamydia, duo hiv neg at 28 day, hep c, a, b, trichmoniasis, negative IGG bloodtest for herpes at 8.5 weeks also negative swab for herpes and syphilis (BUT) very concerned about this being herpes or hpv infection.

I am currently prescribed Cipro and Metronidazole combo medication. I notice after 2 days my urine is dark orange with a sappy orange discharge during the night.

The only thing about your post that concerns me at all is your description of the small oval hole near the rectum.  You said you had a negative swab test - was that from the hole?  Any opening in the skin that discharges pus as well as anal discharge should be evaluated right away but I'm thinking maybe that has already happened? 

A negative IgG test at 8.5 weeks is probably 85-90% assured that you don't have HSV 2.  I like a final test at 12 weeks. 

I hear that you are having some generalized symptoms but most often, those do not represent herpes infection. 

I would encourage you to have any sore in the boxer shorts area to be evaluated by a professional, but the negative IgG, the fact it was a single encounter, and the fact that you've had no penis lesions all lead me to think it is very unlikely that this is a herpes infection

Terri

What was the index value on the positive and was it HSV 2 or HSV 1 or did the test distinguish between the two?

Terri

You definitely need more information. You need a test that accurately separates type 1 from type 2 (type specific IgG) and an index value for each.  You can order this test online for yourself if your doctor did not order the correct thing. 

Terri