The needle might be worn and letting too much fuel flow in. When the carb was rebuilt, was the needle arm put in correctly? I was having similer problems with my 89 Wavejammer 500 (which has the same Mikuni BN38 carb.) I rebuild the carb and found the needle arm was put in backward (little dimple was against the needle instead of against the spring.) It ran but was hard to start, even worse when warm. Switched the arm around during the carb rebuild and it runs perfectly now! I have pictures of what I'm discribing in my post "1993 WaveBlaster and 1989 WaveJammer project" found in the vintage ski threads. Hope this helps!
1993 Yamaha WaveBlaster 701
1989 Yamaha WaveJammer 500