929 Stutters from idle when warm
I have a 2000 929 in which I have replaced the engine with a 2001 engine that was from a bike destroyed in a fire at a dealership. Replaced everything inside that melted (cam guides, etc). I did put the tensioner lifter in wrong the first time which caused it to shred the plastic from the tensioner. Replaced that again, got the engine running.
Now, when I ride, everything starts fine. engine idles smooth, accelerates good, etc. Once it warms up though, things don't work so well. It begins to idle rough, and when I start from a complete start, it stutters / bogs down significantly until probably 4-5k rpm. Once there, it seems to run well again until I have to stop again.
I have not checked the voltage when warm, but the battery is brand new, as are the spark plugs. I have not pulled them yet to look at them, but I am not sure they could be intermittent the way this problem is.
Any advice on where to start troubleshooting would be appreciated.