Seeing a Chiropractor is fine, but have you had any imaging of the troublesome shoulder done? I didn't see if you had in your OP, my apologies if you did. If this is sticking around this long after being treated by those doctors maybe there is something amiss that a manipulation is not helping. A ligament tear or such, say. With your experience and a custom built and fitted bicycle I'd doubt it is in the bicycles fit, unless you have inadvertently changed something like a seat position. Just a thought, if you don't care for imaging or such, that is your business, not mine.

Bill