I'm not a big expert on two strokes...

but it sounds like either 2 things (imo)

1: It could be running lean because you dont have your airbox fitted (check your jetting, needles if your modle of caries have that and check your mixture screws for idle (again if your model has those)

or 2: you might just be simple enough that you might need to re adjust your idle again after your rebuild.
_________________
1991 CBR250RRL mc22 modified.