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Thanks for the assessment OpticalFlow. It didn't occur to me that something other than the scoring on the rear lens would cause the softness. I will have to think about my options.
Well, the first thing I would test if there is a problem apart from misfocusing at all.
I would image something like a large sheet of newspaper with fine print at an oblique angle, best with base iso and high shutter speed (or tripod if you don't have enough light). Because of the oblique view angle some part of the print will be in focus if you're not completely off. Then assess the sharpness on the in-focus part of the image.
Why am I so confident that the visible scratches (or fungus) on the rear element doesn't cause "softness" ?
Have a look at this Canon FD 55 1.2 (link to a post by "hinneker" in a German forum: http://www.digicamclub.de/showthread.php?t=12322&page=13&p=143113&viewfull=1#post143113 ). This is a very comparable lens with much worse damage to the rear element. On the following pages you can see a few more pictures taken with this damaged lens. The defect is only noticeable in the out-of-focus highlights of the bokeh shot (http://www.digicamclub.de/showthread.php?t=12322&page=13&p=143113&viewfull=1#post143113) and when you have light sources in your image.
Maybe you're lucky and not much is wrong with your lens at all. That would be the best outcome. Otherwise or if you still decide you're not happy with it drop me a PM, I might be interested.