I put together a '98 GS500e and for the life of me I cannot get the carbs right. New boots/orings so that should not be an issue, and it's still sputtering and s[itting and off to the races when it fires up.
Whenever I rebuild my carbs on anything I always disassemble them completely, take them to a local lawnmower repair shop, and he actually ultrasonically cleans them. Then I throw all new jets in and everything. One time when I gave him a craftsman flojet carb he actually dialed it all in for me free of charge. Only charges 25/carb. if there's 4 though he'll clean rebuild and sync them for 200. guy's been doing it for eons.