your shaft looks fine
to me (no joke intended), same as all of mine look when i strip them down. water seal looks good from a distance, i have not found a problem on any of mine either. they are not exposed to water like a 1-18 or a dishwasher seal, neither do they turn at nearly the rpm as a dishwasher motor nor as much so i would guess a rollermatic water seal would last a good while. lets face it the water level never gets up to seal level in a rollermatic even when it is throwing it's water so thats good!
your outer tub looks good compared to a couple of mine and mine cleaned up and repainted beautifully so you are in good shape there!
yes, looks like you got it back together correctly, there is not that much to assemble. tub goes in, tub nut goes on and then bellows start.
unfortunately i still do not have an answer on how to loosen those stuck agitator nuts off the pipe nipple part. you and i have the identical problem here. i have had mine soaking in pb blaster for a week or so here.
i find when i am stumped the best thing is to walk way from it for awhile, weeks even, and then come back fresh to tackle it again. i have been working on my kd-12 and my sears top loader this week, and a frigidaire dryer.
i am going to try holding agitator nut in a vice with a 1/2 inch socket and extension. then i will try to turn nipple with a vice grips. i am also going to apply heat to the nut using a propane torch after i wrap inside of jetcone with roofing tin flashing as a heat shield. last thing i want is to melt that agitator! when i work on it again will post results here.
good luck with it, keep me posted if you discover how to get that nut off that pipe nipple.