I wanted to post another follow up. It's been over two years since the onset of my initial symptoms.
I was diagnosed with a syrinx in my neck, and a smaller one in my lower back.

The good:
My body has adapted the best it can to the new circumstances. The soft flabby pectoral and tricep on my right side are better, and flexing them no longer results in immediate cramping. I look and feel more symmetrical and when flexing my right pec it now behaves almost the same as the left. I'm able to do in the neighborhood of 50 pushups and 20 pull-ups, which is almost back to where I was before this all began. I know the problem is still there, but other muscles must be compensating and filling in, because it has improved which was initially diagnosed as impossible.

The bad:
If I push it hard with weights, about 24 hours later I will have an unnatural feeling severe headache which will last a day or two. Bodyweight exercises are fine, but heavy bar weights will set it off.

I think I was born with the syrinxes in my neck and back they've just grown over time. The only other contributing factors may have been several neck whiplash car accidents growing up. (Nothing drastic, just some neck pain for a few days afterwards.) I also have arched my back when bench pressing for many many years when maxing out.

I hope that anyone reading this still suffering does not lose hope. I didn't. I've been doing P90X continuously for the past year and pushed it as hard as I can with bodyweight exercises and calorie counting. It has gotten better for me and I hope it does for you too.