I had my first ever two unprotected vaginal sex with a new partner with bacterial vaginosis (because I can tell from the fishy odor and was diagnosed by an OB) exactly 24 to 25 days ago (it was 2 days) on Dec 17-18. Sessions last 3 minutes each. I got a sore throat on the Dec 24. Then I experienced near constant tingling throughout the day on the right side of my urethra, near the base of the penis on Dec 26 that I experience until today but has lessened in duration and intensity. I developed cough and colds on Dec 28 which is almost gone as of today. I have gotten 2 IGM herpes blood test for hsv-1 and hsv-2 on Dec 30. The test came back negative. I do not have hsv-1 or hsv-2 prior to this occasion and I never had any other sexual partners. On Jan 5, I went to a urologist and explained the same symptoms I presented here. He let me get a urinalysis and he said there was nothing to see, but I am only assuming this tests for chlamydia and gonorrhea, but not another major STD which is syphilis. He then told me to go back March for an HIV test. 

I only had common colds and the tingling on the right side of my urethra near the base of my penis (and sometimes I believe radiates to the testicular area but very mild and brief) as symptoms. I never had any flu symptoms of fever, headaches, extreme fatigue, rashes, and etc. I never had any discharge or discomfort when urinating, I never had lesions appear on my penis, but I have one small pimple like object on the glans of the penis. I believe it was already there even before the exposure.

I wouldn't be worried about STD's anymore if it wasn't for the constant tingling in my urethra. Could it still be very mild dormant herpes? Could it be HIV? The IGM test should have theoretically picked it up by then, but I don’t know if it can be a false negative. Please do advice.

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Welcome to the Forum.  As you probably know but are trying to work around, clients on this site are not permitted to request who responds to their questions.  All questions regarding herpes go to Ms. Warren and Dr. Handsfield and I split all other questions.  As it happened, today I happened to pick up your question.  As an FYI, having worked closely for more than 35 years, Dr. Handsfield and I never disagree on the content of our replies although our verbal styles vary.  I will be addressing this question.

The encounter you describe is low risk for STI.  Most people do not have STIs, most exposures to infected partners do not lead to infection and it sounds like your recent partner has been recently checked for STIs (if she was checked for bacterial vaginosis, she was likely checked for  other STIs as well)  all of which combine to make STI quite unlikely.  Urethral tingling of the sort you describe is not at all suggestive of herpes and is not a concern.  while urethral herpes does occur rarely, the duration of your symptoms is incompatible with herpes and to have isolated urethral herpes without external lesions is quite unusual.  Should you have future concerns, I urge you not to test with the IgM test.  These tests are renown for their high false positive rates and misleading results.  You got lucky with your negative results. 

Urethral symptoms are sometimes difficult to characterize.  The most reliable symptoms of urethral/penile infection are abnormal penile discharge or burning on urination, neither of which appear to be present for you.  From all that you have described, it is unlikely that this is an STI however several comments and a suggestion or two:

1.  If the urologist did only a urinalysis, then to be absolutely sure you did not acquire and STI such as chlamydia, it would be advisable to have a urine test for gonorrhea and chlamydia.  This is a different test than a urinalysis which looks for the presence of white blood cells and a variety of chemical abnormalities in the urine which can lead to the diagnosis of a lot of different problems. If your urinalysis did not show WBCs STIs are unlikely but to be 100% sure, testing for chlamydia and gonorrhea would be a good idea and provide you with assurance (these infections can rarely occur without the presence of WBCs).

2.  It is not clear that you had a blood test.  while your symptoms do not suggest HIV or syphilis in any way, if you did not have a blood test, you were not tested for these STIs.  If you choose to test for these unlikely possibilities, the proper time to have a blood test would be 4-6 weeks after your encounter.

3.  Is it possible that you are looking for symptoms and, as a result, becoming aware of normal sensations which normally go unnoticed.  Anxiety focused self awareness can cause the sort of sensations you describe. 

I hope these comments are helpful.  It is unlikely that you have an STI from the encounter you describe.  EWH