Genital Pain

[FreakingOut1992]

Hi I am a 21 year old heterosexual male and about a month ago I had unprotected vaginal sex. A few days after this I began feeling a burning sensation at the tip of my penis, it would flare up sometimes but would never actually go away. I thought it was an STI so went to get tested and the results came back negative, the Dr said it could just be strain or due to the fact you haven't had sex in a while and to give it a few weeks and see if it gets better. It has now been a month now and the pain is still there, it will go away sometimes but then will come back and if anything feel worse. My partner also got tested and she came back negative as well, so my question is what might be causing the pain?
In interest of full disclosure I have also had a sore/inflammed throat, chest pains/tightness for the last week as well and a higher than normal amount of mouth ulcers. I don't know if they are related but they all appeared after my sexual encounter, prior to which I had never had any of these problems.

[ill13632]

I have shooting pains in my ducts/vesicles and pain on erection.  a few years ago I had unprotected sex and a jock itch rash, purple.  I never had these problems before like ED.  

[FreakingOut1992]

By yeast do you maybe mean thrush or just an imbalance in my flora levels due to a reaction or something?

[Caryopteris]

I'd take a prebiotic to see if your flora is just off, plus use neem soap.  Neem will help control bacteria, fungi, and viruses, so maybe between the two, it will get you back to normal.  Avoid eating sugar, like soda and juice.  Basically maybe you have a little yeast going on.  

Different people have different skin and genital flora, so that's why it's so important to shower and WASH HANDS before sex.  And of course, using a non-latex condom would be wise.  If you used a condom part of the time, you may be having a latex allergy I suppose.