If the bumps are still there, I'd bring it up,. But most doctors would typically notice something abnormal, so perhaps it is just ingrown hairs. There's no use in worrying until you know for sure. Seeing as how your boyfriend has absolutely no symptoms and your doctor didn't recognize genital warts, perhaps you do not have them. Almost everyone's body (except for a rare minority) fights off the virus eventually, but removing warts is still advised.
There's a lot of good information about the HPV test here:
http://www.thehpvtest.com/
I went to the doctor this morning and had a pap and STD tests, and some bloodwork, (I also got guardasil) the doctor didn't say anything about the visible bumps, but I'm going back in about 2 weeks and I'll ask her some more questions. The HPV test will take some more time but I'm negative for other STDs. The nurse suggested they were ingrown hairs or cysts but she didn't see them- they're in between the vagina and anus not on the labia where its more easily confused with something else.
I have a low immune system, I've been catching many things since I've been with him and I have had chronic tonsillitis for 5 months and get a fever about every 3-4 weeks. So I need to wait a bit longer before I know if they will spread and need to be removed, or if I can fight it off? And will the HPV culture only test positive if its on the cervix (or only if its the high-risk type?), and not if its on the labia or vagina?
Developing warts on the mouth is highly rare and typically only happens in cases where people have HPV in conjunction with severe immune deficiencies such as HIV or cancer. Many people carry wart strains of HPV and never develop a symptom, such as your partner. It doesn't mean they're any less infected, the virus just reacts differently in their body. It is safe for him to have sexual contact with you, seeing as how you both already have HPV. You are not a risk to him and can not reinfect him with the same strain he already has, when his body suppresses the virus he will develop an immunity to it. But once you have on strain of HPV you can never catch the same strain again. I'd also recommend him seeing a doctor and getting thoroughly examined. Chances are he may have had or had warts and they're just too minuscule to detect (they can be so small they're invisible to the naked, untrained eye) sometimes.
Have you been officially diagnosed with having warts yet?