Nothing more disheartening than having issues after a rebuild. I had a Suzuki Vinson last year that was smoking bad. I put new rings in it (nikasil cylinder so it still looked new) and fired it up and it still smoked. I went out and rode it hard for a bit and the smoking cleared up.
welllllllllllllll...lol, first..yes..chit happens !. but if a person takes their time, uses the correct parts ( or just makes sure parts will work ? ), then you worry about if your work was done right ?. I've been down the same road as the OP many times !, it sucks to rebuild something, and it not run right ?, or something else pops up, that you had no clue there was a problem, or what caused it ?, until you discover it !..lol. had this problem on an old trx350 rancher many moons ago, damn thing ate my lunch and some !..lol. little did I know, that the valve seat could work it's way out of the head once warm/hot ?. I replaced almost everything new with oem, and it still made a rattle when warm/hot ?..that's when I looked into this matter deeper, and found out Honda had a defective head on some of their trx350 rancher heads !..lol.