Coloposcopy-No period 4 months following.

I'm trying to avoid another doctor's visit if possible, as the coloposcopy was so expensive even with insurance.
So here is my history and concerns.

My entire life I could go six months without a period then have it for almost a month straight if I was not on the pill. This is how it was throughout highschool until I went on the pill when I was 18. A few years ago I gave up birth control for two years and I only had 4 periods during that time. However, when I'm on the pill I've always been like clockwork on a 28 day cycle and I've never missed a period. (I'm 28 years old). I have been on the pill for two years now and take it at 8am every morning to an alarm set on my phone.

This March I had a coloposcopy which resulted in the finding of a very small area of a non-cancerous HPV, I have no other STD's or health concerns and I've been tested. The doctor told that as of now I would not need any treatment for it and if I use condoms for a year that the HPV would probably disappear, maybe even sooner as it was such a tiny (his exact words) area that was infected with it.

Following the procedure, I was told to expect discharge that was yellow due to the adhesive used to glue the cut or whatever they did during the procedure, and was told that some of it would come out later and look like coffee grounds. That never happened. I never had a funny discharge or any bleeding following the procedure. However, I did cramp for over a week afterwards. I waited the two weeks following the procedure to return to having sex with my partner. When I did it really hurt the first few times, then went back to normal. Since the procedure even though I'm on the pill I have skipped four periods. I've taken tests every month and no I'm not pregnant. In addition to this, sex in the past month has become more and more painful. My boyfriend is an average to large average penis size, but now feels huge during intercourse so much so that it has become unenjoyable and painful, but looking at him, he hasn't grown. He says I'm tighter feeling, and he is worried that something is really wrong because the change is so noticeable in how I feel in my vagina. Any experience with this, tips, advice.

I eat healthy, organic, foods. I exercise almost everyday, I'm using condoms. I have no other health conditions. Why would my periods suddenly stop? Why would my vagina walls change so much? Does that usually happen with a coloposcopy? Is there anything I can do? What are other reasons that sex could be becoming so painful and my vaginal walls would change, I'm missing my period etc.? No he is not cheating on me, and talking to my old ex he must have carried HPV because his current girlfriend also has it. I've been tested for STD's after each relationship and I've never tested positive but found out that they usually do not test for HPV because it would show up on pap smears. I was re tested for other STDs when they did the colopsocopy and have nothing. I know my current boyfriend hadn't had sex for almost a year before me and we've been together 6 months. I'm just trying to find an explanation but cannot come up with anything. Any thing would be helpful. Thanks!