Well it's been a long time since this post, and it's been a long road, but I finally have this thing sorted out! Wanted to post back on this thread in case other people experience similar issues in the future. I've actually experienced several issues with this bike, all of a similar nature, and I'm pretty sure they all happened independently. I was about to throw this thing to the curb but finally (knock on wood) have it running great.
The original problem was actually an air leak at the intake manifold. The random periods of running poorly after it had been sitting turns out to be due to me sitting in the bottom of the "seat" between sections. My weight on the airbox pushed on the back of the carb, which caused a gap to open between the front of the carb and the intake manifold. It was so random because I didn't always sit on the bike during breaks, so sometimes it was sealed and other times it wasn't. I accidentally discovered it one day when it was running and i put some weight on the "seat" and heard the bike immediately bog. I replaced the intake manifold and clamp, and then it was running great. Figured I was home free...
After a few rides thinking I had this thing fixed, random performance issues appeared again. This time it was similar in nature (random periods of bogging and poor low end performance after starting the bike) but definitely not an air leak. After some troubleshooting I realized that I could start the bike, test for bogging, shut if off, start it again, and it would be perfect. I decided to replace the CDI box since only something electrical seemed likely to cause such drastic performance changes only seconds apart after a restart. New CDI box installed, problem solved. I probably rode a few months without issue. Once again, figured I was home free.
A few months back I was on a trail ride and was working up a long hill climb of switchbacks, and all of a sudden I lost significant power. I was almost holding the thing wide open and barely made it out. I tried a whole range of things (fresh gas, new spark plug, carb cleaning, carb tuning, checking for air leaks, my old CDI box, etc.) in the time since but nothing was making any difference. When I had the problem I was up at 9000', and then the rides after that were here in New Mexico at 4500' plus 90F degree days, so I was convinced I was experiencing a finicky 2 stroke carb and my problem was related to jetting. During a test ride yesterday, doing some throttle roll on's down a fire road, the horrible performance continued. The thing was SO down on power, I was convinced the thing was going to quit/seize/blow up at any second. I was ready to start looking for a new bike since I had absolutely had it with this thing. Just before I was going to shut the bike off, I passed my hand behind the exhaust and realized I didn't feel much flow coming out. I held my hand back there, rev'd the bike, and not a noticeable change. I had never done this on my trials bike before, but on my CRF450R that sucker moves some air, so something seemed off. Today I removed the slip-on spark arrestor from the muffler and saw a PLUGGED screen. Muffler packing had come loose and lodged itself in the spark arrestor greatly restricting the flow. Someone in an earlier post had mentioned to check this, and even though that didn't apply to the first two issues I had, it did on this one! When the bike had the sudden power loss on the trail ride, that must have been when the packing came loose and got lodged.
Today I started the bike with the spark arrestor off and that thing ran like a bat out of hell. Super crisp, tons of power, and I was smiling again. I pulled out all the packing from the spark arrestor, took a wire brush to it, soaked it in Simple Green, and then finally hit it with a torch to burn away as much carbon buildup as I could. It's nice and clean now. Reinstalled and I'm back up and running.
Hopefully nobody ever experiences all of these issues back to back to back like I did, but if you do, I hope something in this post helps you find it faster than I did! Here is hoping to some better luck for me with this bike moving forward. I'm tired and just want to ride.