It's been about two weeks since my mouth has hurt. I've had pain in my cheek, near my teeth, and in my gums, all in the same general area, so it's hard to isolate one source. About a year ago I had an inflamed gland in my cheek and an oral surgeon put me on amoxicillin which treated the infection. I thought that's what this was originally, but then the pain got a little worse. It's a pinching pain that literally goes on and off every few minutes. It usually just gets sore for a little while, but at times it can wake me in the middle of the night. Any ideas?

This could be either a periodontally related problem (affecting the gums and bone around the teeth) or an endodontic problem (root canal/nerve). Or it could be a combination of the two. If you have not had a full exam in a while- I suggest, as the first step, to see a general dentist for a full exam, or for this acute problem that you described, then a full exam after this is treated.
It is hard to accurately diagnose problems such as this without actually seeing the patient. Radiographs are very revealing too. You'll likely need them before a definitive answer can be arrived at for this problem