I am emulating Kirby 64: The Crystal Shards using Project 64, but every ROM that I have found says "Issues (plugin)" under the status column. When starting the game, the controls work up until the point when I hit start new game, then start works, but everything else just stops working. Any thoughts on this issue?
Kirby 64: The Crystal Shards is listed in Project 64 as "Issues (Plugin)" because, according to the Game FAQ included with the emulator:
Missing life meter (eggs) on HUD - we have heard from users that after the first boss the meter is displayed normally. Or the problem may come and go at different points in the game. Exact cause is uncertain, very likely something in the core.
Project64 184.108.40.206 beta fixes this issue, but you'll have to be a donor to download the beta. If you don't want to spend $20, then Mupen64 will fix the issue.
As for the controls, Kirby 64 is one of the oddballs that uses the D-Pad instead of the control stick. If you're having trouble with all the other buttons, check out NRage's Input Plugin.