What kind of stretching are you doing?
And is the pain just localized in the center of your lower back?
I'm not sure what the stretch is called, but if I were to describe it I lie face down on the floor with my arms in a pushup position, and push myself up until my arms are fully extended, so that my back arches while my legs remain on the ground. It seems to hit my lower back pretty well.
I also do posture stretches where I touch the ground with my hands while sitting, then sit back up and sit with an exaggerated posture, and then return back to a regular proper posture.
The pain is only in my lower back, a bit above the tail bone. The pain was more in my right side before, although over the past couple of weeks I haven't noticed that as much. No pain that I can remember in my butt or legs or anything.
I think one of the issues that has extended the healing process is the fact that I commute to class five days a week, which involves 3-4 hours of commuting per day where I'm sitting on a train or a bus, and when combined with the sitting in class that I do I end up sitting for much of the day. I try to stand when I can, but the opportunities are fleeting.
I've also been taking naproxen pills twice a day, and occasionally using a heat pack on my back. If there's anything else I could do I'd love to know. I'm only 20-years-old, I don't want to deal with back problems so early in my lifting days.
EDIT: I injured my back while squatting 315 for reps. At the last rep I think I arched my back inwards too far, and I felt a tweak I hadn't felt before. My back hasn't been the same since, although recently it has gotten better.
And no, the doctor hasn't recommended an MRI, which I thought was odd considering it would show if I slipped a disc or something, correct? I didn't ask him about it because I'm insured under my parents still, and I don't the ordeal to cost them extra money.