Today I took the time to look a bit deeper into the issue. Had bought me a rear master repair kit at OCT, as I was sure the issue was there. It is btw. a PS12, which has something like 12.65mm piston diameter, so a bit more than a 1/2 inch Jap, but not critically more. That made me think, as with the 1/2" on the Jota, everything is working fine...
So - put the bike on the lift started to losen the screws on the master when suddenly I thought - what if the problem is actually the (used, 36 years old) GSX-R caliper...? As I anyway first pump out the caliper pistons to a certain degree when I exchange the master so that enough fluid is in the caliper that I can send back up to the master when I re-install it to get rid of all air, I checked how the pistons are moving. Or better: one not.
I blocked the moving one to see if then the other one would be moving, removed also some air that still was in the caliper

by the 2nd bleeder so that finally, the second piston started moving. Great, I thought. At least, until I tried to push it back in... No freaking chance!
OK - so, what to do... Getting a repair kit for the 36 years old GSX-R 1100 caliper on a Saturday is impossible. Scratched my head a while until the spare caliper sprang to mind that I had bought for the Motoplast project years ago and that was still on the shelve. Took it out, removed the unnecessarry mounting point, cleaned it, put in new brake pads and mounted it to the 1000 SFC, bleading it thoroughly several times. Everything else put together again and test drove it up and down the road.
It was defenitely better than before, but still not as I wanted it though it improved after several braking attempts. So - back to the garage, master repair time! It made a creaky sound anytime you pushed the food-lever, so I thought it's best to be repaired, too.
Replacying the piston is really straight forward and no big deal, as long as you have some tools that you need (see the brake master repair guide in the Wiki-Section).
Master back on the bike, bleeding it again several times until now air comes up anywhere. Bike off the lift, testdriving it up and down the street several times - works! Not blocking the rear tire really like on the Jota, but it definitely is now stopping the bike! Might improve over time once the new brake pads have seated correctly. We'll see if it improves. Currently happy with the results so far.