It has been 40 days since my last period but my cycles are usually around 30 days (29-31 days). I have been having cramps and clear vaginal discharge lately and heard that this may be a sign of pregnancy; however, I have never done anything that may result in pregnancy, ever. Though I have had missed/irregular periods before, it has now been 5+ years since I first started menstruation and my cycles should have settled down, right? Additionally I am fairly certain that my periods have been regular for the past two years or so at the very least. What is going on? Should I be worried?

If you have never done anything, that could result in pregnancy, then you are a virgin and have never had sex. Or at least you have not had sex in the last cycle prior to missing this period.
Then you can not be pregnant.

But there are 100's of reasons to be late, or even miss a period sometimes. If you wait and next months does not come, time to sch a doctors appointment.

If you've never had any sexual contact at all (that includes dry humping without a condom, a guy jerking off near your vagina, or jerking off and then touching your vagina afterwards, and more) then pregnancy is definitely out. Sorry to be so graphic, but it can happen. The virgin birth of the bible is really not at all a miracle, it can and has happened. Penis doesn't have to enter vagina for it to happen. Albeit rare, it does happen all the time.

How old are you? You stated that you've had your period for 5 years now, and they have been irregular during those 5 years. So this isn't anything new then?

Fact is, some women never get a regular period. For some women irregularity is the norm. My mother, who had me in her early 30's, never had a regular period. She had, if she was lucky, one period a year. That and other problems, made it very hard for her to conceive.

Irregular is the norm for many many many women.

Now, if you think there's something going on, you need to see a gynecologist. You really won't get answers online. I can give you a list of things that could be causing an irregular period. Do you have a few days to read it? I'd need a few days to write it. Even if you want the list, no way to know which, if any, are the cause of your irregular periods.

You'll need testing done, and only a doctor can do that. So if this is a concern for you, see a gynecologist. Chances are there's nothing wrong, you're just one of the many women that have irregular periods, but if this is a concern, my advice is the best anyone can give you.

Good luck. :)