OK, three month of PE even light PE will effect the state of your flaccid penis. You can expect it to seem less flexible. It may not fall in the same way. All this is normal.
Having too great an erection level is more likely to produce immediate and visible injury.
So there’s no pain in the testicles?
You could definately locate the pain in your penis and it has definately moved since then? With a low throbbing pain it can sometimes be hard to locate the centre effectively.
Night time erections are easily missed, even when you are having them as normal. You can check this by wrapping something that will easily break when your penis is erect around the flaccid penis. People use a row of stamps or some tissue paper for this.
A constantly flexed muscle is unlikely. You can probably test for this by flexing and seeing if that makes a difference.
Don’t be too worried. I know it may seem bad but from what you’ve said so far I think this will be transient. You did the right thing by going to a urologist. Did you tell him what you had been up to?
Just confirm for me. Have you managed to get a full blown erection since this started?
The color of you penis is normal right, you are getting reasonable blood flow?
Have you been doing anything with your penis since this happened? Massage etc?
How old are you?