Welcome, can't wait to see pics of your project.
Sorry, didn't respond sooner, but I don't really have great suggestions for the shifting issue. My thought is bent shift fork or possibly the spring that pushes the fork into place. I really doubt actual gear issues, but could be wrong.
I have installed the Factory Pro shift detent kit on mine, and do like the crispness of the shifting now. It wasn't bad before, but I could catch neutral from first and now that never happens. Part of my problem is probably my size 14 clod-hoppers, but can't do much about that-
Also, I had put on a set of Raask rear-sets and the linkage angles caused some shifting issues. Ended up taking them back off because of that and the rear brake was affected as well. You could just have a linkage issue, but the stock linkage is pretty bullet proof and I figure you would have seen that.
Anyhow- Good luck and post pics!