I assume you now have spacers between the springs and damper on the lower mount. When you rebuilt the damper what oil did you use? This can be critical to a good set-up. Most suspension tuners say " soft springs and firm dampers" and that has worked for me for forty years. The friction seat stays are a hangover from Series A and B bikes. Light machine oil on the damping fabric stops squeak, judders and still gives a smooth damping for the passenger. You say you have 1/2" each end of bump stop. That doesn't sound right. There should be a bump stop at the top of the piston but not 1/2". With modern oils I use a 3/8" Nylothane bump stop. IF the damper is compressing to full travel then you have to do a few things; but one at a time. First I would put heavier oil in the damper. Then I would think about changing one spring to a heavier one. Before doing anything you need to measure suspension sag; both static and with you sitting on the bike. This is critical for a comfortable ride. Cable ties are your friend here. Happy days.