I've been keeping up with your thread,and I think Tews19 is right, you've gone this far into a rebuild and have found allot of oxidation in the cases. It would be a shame to put it all back together only to find that shifting forks are rusted and needed cleaning(poor shift/no shift), or tons of rust that could have been removed before effecting other parts, Piece of mind that comes with the inspection all bearings and mating surfaces, removal of rust deposits from all gear surfaces, examination of partials in the oil pan, changing out shifter and kick start seals, pan seals....clutch,you'll want to take that apart, get the rust and spent clutch particulate out of there. This is stuff that won't be costing another thousand dollars that you can take care of, such a waste it would be to come this far and fail. You are in a good position right now to do this and the choice is up to you. I'm sure there is enough knowledge here to help you through it. I would most certainly take the lower end apart, inspect, clean every part,then this machine will never be a stranger to you and you'll know what to expect with confidence.