I have a 95 f3 I picked up cheap but butched.The problem is the evap system and the fuel can mounted under the swing arm was removed. the fuel lines run from the tank to the pump to the carbs,the bike runs great through 1st gear ,when you hit second gear it feels like it's starving for gas and sounds like a v-twin. I've also tried running the fuel line straight to carbs and bypassing the pump but the result is the same.
ANY HELP OR IDEAS WOULD BE GREAT...

 

Have you tested the pump itself? Saying it does the same thing with or without the pump inline sounds like the pump isnt working. Could be carbs WAY out of sync, fouled plug/s. Check the pump!