Stroke dillema, what should I do?

I've recently returned to swimming after about a year and a half absence. It all started when I ruptured a disc between my C6 and C7 vertibrae, causing severe nerve impingement (perhaps damage) in my right arm. Before my injury, I would warm up with a 400 which would hover around 7 minutes. Of late, my time for this benchmark has been around 7:30. Also, my PB for the 100 free was 1:22. My most recent best in that event has been 1:30. Yes, I know I'm not that fast but I don't race (except for occaisional open water swims) and my only competitor is myself. All in all, I've been pretty happy with my progress. Then recently, I started alternating my breathing. Two things happened. I went faster and I also got horrible side stitches. Yesterday, I tried doing a 100 breathing entirely on the left (my "alternate" side). I couldn't complete it due to the side stitches. Today, I switched sides (from right to left) halfway down the 25 yard pool. My 400 yard warmup came in at 7:06! But my side hurt a little. I discovered that my pull count is way lower when I breath on the left. I basically have found that I'm faster if I breath on the left if I can keep my side from hurting. But it's very hard to keep my side from hurting. If I could, I might even break 7:00 for 400 yards. I have no problem doing a 100 in less than 1:45 breathing on the left. Has anyone else had this problem where they get side stitches (aka Exercise-related Transient Abdominal Pain or ETAP) when they switch breathing sides? Has anyone switched their dominant side for breathing? Will training or conditioning overcome the side stitches? Is it worth it to try?