It's possible that your hose has delaminated inside and the lumen (the passage) has become narrowed (not blocked) and may-not be allowing a full retraction of the calipers once you release foot pressure. That most-likely would put a lot of drag on the wheel, and the caliper and rotor would be hot! I think this is one of those times I'd be investigating everything from one end to the other. It sounds like you've done a pretty-thorough overhaul. You saw on one pic where I removed the entire system from a SOHC Honda, to work on it. That was more because of it being in a storage facility and you aren't supposed to do mechanical work. I don't want to get in trouble there, so I removed the front brake system, did the repairs at home and re-installed it.
I may be lucky, but I've never had a caliper so-bad that a seal kit didn't fix it, though I have replaced on a car, a 'loaded' caliper (remanufactured caliper and new pads).
What I see when I release pedal pressure, is a small amount of retraction from the caliper. Do you achieve that? The radial run-out of the rotor will also push-back the pads, even if it's only thousandths of an inch. It's enough to allow free-turning of the wheel, if you had the rear wheel elevated (centerstand or track stand). Is your drag significant-enough that it presents rolling-resistance to rotating the rear wheel, off the ground?
The Brake Crafters kit looks decent as it has SS pistons.
https://www.ebay.com/itm/2225331069...Yamaha&hash=item33d001bcf4:g:jgAAAOSwA3dYUHuyIt's worth a try. I think I'd make sure that the brake hose doesn't have any issues first.