Gary I’ve done exactly what you are talking about. Don’t be discouraged. Given enough time you can overcome any issues. I bought a 1999 CR125 bike off craigslist for $800 bucks. I tore the motor out of it, kicked the rest to the curb, tore down the motor, replaced the bottom end and top end and it worked perfectly for me.
Then I went ahead and replaced the 5 speed gearbox with a used 97 gearbox from ebay. $300 bucks.
Fact of the matter is, Honda parts cheap and widely available. Also, new parts or old, they will break and wear out on a kart. Karts are very hard on parts, and unless you have loads of money to pay someone else, you will become an expert at fixing the motor yourself.