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What does it do at the ends of the cassette?
Have you used the adjustment mode and moved it fully the other direction to see if it changes/rubs? I've had it before that the hanger was bent and I'd overcompensated so much with microadjustment I was running it wholly in the other gear, next to the one it "thought" it was in.
If you really want to start from scratch then the service manual for your model on Shimano site.
I got new wheels and it was overshifting so I tweaked them but I can;t seem to nail the shifting now and for some reason when I whack it in the 5th gear and try to use the micro-adjust to make it rub against the next gear as per the instructions, it doesn't seem to ever do it. Makes me wonder if I've fucked it with the limit screws.
Just want to go back to day zero to start again.