Sounds like you are totally running out of fuel or spark. Not sure if incorrect jetting or anything else mechanical (valves, springs, etc) would make it totally shut down. If it were something like that, I would expect it to miss but not cut out completely.
Could it be something simple, like your fuel system needs to be vented/non-vented, etc? Since you changed the fuel system, you could be doing opposite of what is required.
I have mounted my fuel pump and filter below and behind my cell and about 1' from it. So it is pushing fuel to the pump. The cell is vented fine, because I can fill a gas can pretty quick with just the pump running.
Is your pump by the tank (push) or by the engine (pull)? Should be closest to the tank for maximum fuel delivery.
Can you reproduce the problem by just mashing the throttle when you standing still, or does it need an actual load on it to do it?
