Thank you for your input!
On this forum we have a rule against looking at posted photos. In this case, I broke it and glanced at the pictures you posted. I see nothing abnormal about the appearance of your urethra. Nothing is wrong.
Welcome to the forum. But I'm afraid I can't help very much.
First, it is very unlikely you have warts to explain the appearance of your urethra. The urologist's judgement that it was not a wart is highly reliable. Second, genital warts clear up on their own within a few months; it would not persist 3 years. And by the way, even if you had a wart, you did not acquire it during the hand job described. HPV warts are rarely if ever transmitted by hand-genital contact; and warts generally take 3-9 months to appear after catching HPV; 4 days is impossible. If it truly appeared 4 days after that event, it had to be the result of an injury of some sort. But my guess is that it in fact had been there before the exposure. Anxiety does wonders for our ability to recognize and "see" something for the first time that was present earlier.
No other STD is a likely cause of the things you describe. The appearance of a normal urethral meatus is highly variable from one person to another, and my guess is that you have nothing abnormal. In any case, this is a forum strictly related to STD, not to diagnosis of non-STD genital problems.
It is a mistake to be avoiding sex on account of this problem. If you continue to be concerned, see a health care provider -- then trust what s/he says about it. In the meantime, try to stop worrying. It is exceedingly unlikely you have HPV, warts, or any other STD.
Regards-- HHH, MD
I also wanted to add that I noticed that several other men have posted about the same problem on other sites. The penis opening looks like a pair of lips shortly after an encounter, and does not go back to normal. Unfortunately, no one is able to give a solid answer about what exactly caused this to happen.