I attempted to get some training in on an upright this winter. I would ride my mountain bike on a Cycle-Ops trainer for approximately 20 minutes initially and then have to stop because of the same pains that each of you have described. With continued training and enduring thru the pain (my sons' theme had been "no pain, no gain" or "Pain is weakness leaving the body."), I did get up to 45 minutes. The knots only got tighter when they occurred. My son suggested shoulder shrugs - weights in hand. Did that for a while and could push myself to 60 minutes and the pain was decreasing. But finally, I found that the knots, pains were not going away despite my perseverance, weight lifting. So, I switched.
I have upgraded from my mountain bike to a recumbent trike. Very much appreciated improvement. And, of course, my chiropractor is pleased with the change ( he had not found that he could effect any change for me.)
Do again, my solution was to change riding style. I found no satisfactory alternative.