Motorcycle Repair: Carb issues I think, rubber diaphragm, aftermarket pipes

Question
Ok to start I recently rebuilt my carbs and found a hole in the slider while apart I rejected the main jets with new needles and seats. At first I was way over sized but after a few attempts I believe I've got them right. However under acceleration past a certain point it seems to flood out. It rev's high and clear in neutral but in gear I'm only getting between 4-5000 RPM before it floods and falls on its face. I'm checking my float heights now.. But I'm lost past this.. I do have aftermarket pipes

Answer
First off, what Make , Model and Year is the Bike.
What kind of Carburetors are they (Mikuni / Hitachi)?
I can help because I rebuild Carburetors for a living.   www.viragocarb.com
Clearify a couple things. A hole in the slider. Do you mean a hole in the rubber diaphragm
that is on the slide? Because that would be bad. They wont operate correctly with
a hole in the diaphragm. I believe you have installed new needle valve seats and needle valves
is this correct?
What kind of Carb kits did you use? K&L?
Your welcome to call me. My contact info is on my website. Aftermarket pipes lets more air flow through your Carbs and require a little bigger size Main Jets.