I've been taking a weight gaining formula daily that is packed with a lot of protein and nutrition to help me put on a couple of pounds. I was wondering if it caused me to miss my period for two months.

Most unlikely. A weight gainer is just a fancy form of milk and sugar. It will help you put on weight, but unless it has some very exotic ingredients (which they would charge an arm and a leg for), it should not affect your periods.

Is there any chance you are pregnant? Has your exercise pattern changed? What about the rest of your food?

It's definitely not pregnancy. I guess it may be stress from my previous relationship etc. But now I feel cramps like I'm ovulating or something, its like my body is trying but it won't happen. Its weird because my stomach is kind of bloated and I have cramps.

What else are you eating? And how much are you eating? If you are trying to put on weight, and you are deliberately over-eating, this could make you feel pretty bloated and crampy.