yo my friend has a 99 500 ninja, and the other day it will struggle to start then if you take it past 3 or 4 grand it'll die.... then you'll get it to run correctly then when you take it out it's just hesitant again.what could be the problem

probably the carbs, check to see if there are any restrictions of air or gas somewhere. Also check to see if all pistons are getting good compression and spark.

If it is not the carb, then check the regulator. They like to mess up on Ninjas quite a bit.