So i have a canker sore\mouth ulcer in the back of my throat for the past 3 days. and it hurts nonetheless. but can this cause stomach aches?

Probably not: The mouth sore should be gone in a couple weeks. If either one lasts i would suggest seeing a physician.

It's possible.: Throat pain can cause you to change your diet as can stress from the pain and uncertainty about the cause so it is indirectly a possible cause. You should get your throat checked to make sure it isn't strep throat, which is highly infectious, but easily treated.