Welcome to the forum! I am by no means an expert but will chime in with my two cents… If you were starting with a motor with a known karting history I would say the repair/rebuild would be relatively easy to deal with yourself; however, I recently watched a friend of mine try to save money by buying a bottom end off of ebay only to have it grenade and cost him a lot more in the end (costly bottom end rebuild in addition to a second top end). I’m not saying to not go the ebay route, but my recommendation would be to pay for a complete rebuild by someone who does this for a living so they can inspect all the components. It’s a lot of $$$ and takes away the fun of learning and rebuilding, but IMHO it’s better than the risk of learning the hard way and costing a lost more $$$.
With that being said, I believe everyone here would use a “slip fit” crank since a stock crank would require somewhat specialized assembly of the main bearings. I’m sure each engine builder has their own black magic but Honda is a world class manufacturer and I doubt they would put their name on anything that wasn’t durable/reliable/consistent (not to mention they have used and perfected their motors for many years).
There are so many nuances about getting the setup that has the cost, speed, and reliability to match your needs I would highly recommend talking to an engine builder. I have been extremely satisfied with my dealings with Musgrave Racing (MRC) and highly recommend a call and conversation with Willy Musgrave.