You are correct in that heavy bleeding and clotting would accompany a miscarriage. Pa is right in that your chances of it being a pregnancy are low if you have been faithfully taking the pill.
As far as a std, yes, your chances of that are lower due to having one partner. I think the latest statistic I read about stds is that 1 in 5 people have one and don't know it. So they said that if you have had unprotected sex with at least 3 people then most likely you have one. While you may not have been with many people, your bf might have been with other before you, who in turn may have been with others before him, and so on.
Cysts are still a possibility. Here are some possible signs of cysts:
ovarian cysts symptoms & signs
pelvic pain - constant, dull aching
pain with intercourse or pelvic pain during movement
pelvic pain shortly after beginning (onset) or ending (cessation) of menses
abnormal uterine bleeding (change from normal menstrual pattern)
lengthened menstrual cycle
shortened menstrual cycle
menstruation, absent
irregular menstruation
abdominal bloating or distention
note: often no symptoms are noted.
Another possibility is that your hormones have changed, and your current pill is no longer compatible with your body.
I would still go ahead and at least call your doctor, explain your symptoms, and see if he/she wants to see you. Better safe than sorry.