I've been riding a Kawasaki ER6F and Honda XR 200 and that has made me realise how bad BMW brakes really are.
That would explain a lot. They both have excellent brakes, I am sure, and the XR200 is so light, it wouldn't take much to stop it, anyway.
I am afraid you are dealing with a situation that cannot be resolved easily or cheaply. I'm thinking aftermarket, multi-piston calipers, here.
And rebuild that master cylinder! The job isn't done if it's only half-done!