I have a 95 Kodiak that I got not running. Even though the carb looked new I replaced it. The motor would run for a few seconds then shut off. Found the CdI was bad so I replaced it. The motor would not run very good at all after that. It pops and misfires like the rev limiter is wrong. I decide to try to run with out the air filter box lid and it runs great. I have adjusted the valves and carb but nothing seems to change. With new filter and lid installed it is crap. Take off the lid and it runs great???

 

"Even though the carb looked new I replaced it. "

You have probably replaced it with one that needs setting up to your machine. My advice clean the old one out by blowing compressed air through the jets, and put it back on. For future reference, always check if you have a spark at the plug first, before doing anything else.