I'd get some emory cloth on it. If it is so bad you are worried about pulling it thru the bearing, I would replace it. Why mess around with this stuff??...Do it once and do it right and replace everything. For this type of work, you need patience and two hands..once you get it shiny and clean, you should be able to better assess its condition and also be able to pull it thru the cutless bearing.
I still have the bronze shaft from my 1977. I'll take pictures and send it to you cheap if you want it. It had some wear from the stuffing box & the shaft log (engine out of alignment for a lot of years apparently.) - I replaced everything aft of, including, the rear main seal when I re-did my beast last year. The shaft is 46-1/4" length...the newer boats have a longer shaft, I am guessing for additional prop clearance to go with the noisy diesels.
I also did not have luck pulling/pushing my bearing out..I cut it with a Dremel tool with a little sanding drum..and then it came out...see pic.