Won't stay running

I have a Yamaha 1100 that when it's cold it will start and idle just fine but as soon as it warms up it wants to spit sputter die shoot out black smoke and all kinds of stuff I've tore the carbs apart clean them put them back together the intake boots were cracked I replace them and it's still doing the same thing I am a Harley-Davidson technician I own three Harley so I'm not dumb when it comes to engines but this thing is just baffling me