To start off I have a complete engine swap, new fuel pump, new fuel filter, new spark plugs, new battery, new thermostat, new radiator cap, cleaned carbs, cleaned cooling system, cleaned fuel tank on a 2000 CBRF4.

PROBLEM:
The bike runs amazing now!
BUT I'm having problems starting the bike if it sits for +5min.
It will crank and crank and crank and then you start hearing it catching. Once it catches it starts right up and runs amazing. I'm thinking its something electrical. It almost seems like there isn't enough spark on startup. I've tried switching the stator from my old motor and it performed the same way. What else should I check?

Its a new fully charged battery, no corrosion at all. Crank time is about 15seconds

 

did you change the fuel filter..
sounds like your not getting enough gas to your pilots..
if it was electrical, i doubt it would start at all..
sometimes when people clean the carbs, the pilots get clogged and thats what gets the bike idling.
i'm probably totally wrong but i figured i'd throw my 2 cents out there..
where is your fuel filter located, in the tank?? if so pull the petcock!

jay