Following up on cfboy's post, here is Lizzie Armistead (World Champion) in full flight.
Lizzie eyes multi-medal games glory | Olympic Games 2016 | Sporting Life
See how her upper arms are close to 90 degrees to her spine, which supports her with the least effort from her arms.
The bend in the lower spine will be rather individual, depends on the person's flexibility and anatomy.
And here she is, gutting it out in pissing rain. Tough cookie.
Lizzie Armitstead Interview: ?I?m a road cyclist in my own right?
See how her arms are roughly parallel to each other.
Given the location of the original pain, I would look at whether the bars may be too wide. The hoods should be roughly as far apart as your shoulder width. (There is some individual variation. Sprinters may use wider bars, for more leverage as they throw the bike from side to side.)
As this is a man's bike, and men's shoulders are usually wider than women's, I'm going to guess you may want to try a narrower bar.
The new upper/mid back pain may mean that the shorter stem now has you too "scrunched up", forced to bend your back too much. I would try going back to the original stem. But only make one change at a time.
Photos would be helpful, but that's what I can think of, sight unseen.
I don't want to discount the importance of upper body and core strength, but that degree of pain in just 30 minutes, when your previous bike didn't hurt you, suggests there is (also?) a fit problem.