you can use the CR125 manual for the model year to check all the various clearances, tolerances and lengths of things. I’d say it is likely that your used crank is just fine and that it may only need a balancing/straightening. That is, if it isn’t your crank that is the problem..
I also wouldn’t bother honing the cylinder if the lining appears fine. Unless you actually smeared aluminum (from a melted piston) up the side or broke off something in there, it should be fine.
this site has info on drilling holes for lubricating the piston. I don’t see any reason why you wouldn’t (unless your race org doesn’t allow it).
BTW – if you’ve never split the cases before. You either need the honda tool to do it or a big f’in hammer (and subsequently damaged crank assembly) and a lot of patience. After the first time, and after honing your crank for future dis-assembly, you’ll have no problem separating the cases.