Oh wow, you are far from stock lol... Now, your CB650 motor and the rear wheel... what wheels are you using, the stock '78 CB550 wheels? I am not sure whether there is an offset like the later CB750's of 10mm or not, but you would know that. Also not sure how much offset your wheel was to begin with vs the CB650 front sprocket. If, after you aligned the front and rear sprockets on the bike by using custom spacers at the rear wheel, that is most likely why your wheel is not centered in the frame.
Now... getting to the R6 front forks, are they the early models with conventional forks (not USD) and the blue star calipers? Or are they the later USD ones? And, when you installed them, were you having to adapt with spacers to fit the front CB550 wheel into them...? Am sure that is the case, and you most likely centered the wheel between the fork legs.
It is a question as to how it rides and handles, and whether the front wheel would be easier to shim over to align with the rear wheel, and if you think it would improve the handling by centering the rear wheel to the frame, which 'should' line up the front also.
Shifting the rear wheel to the right would offset your sprockets, and is there a way to mod the front sprocket to match the amount you would move the rear wheel? If not, then your sprocket carrier would have to be spaced, and this is something I am unsure of, as to whether the CB750F carrier can be used in the later CB550 hub? If so, it has a 10mm offset for the later CB750 engine. Just a thought, not sure if it would work.
Charlie