Jeff,
I had the same problem on a YS 140DZ. I rebuild the pump new diaphram, gaskets, springs and the little valves. The engine would run fine at idel and to about 60% throttle and then air would start coming out of the pump and causing the engine to lean out. I did the same as you and replaced valve cover gaskets and all the o-rings and still the same problem. What the problem was is the pump housing was worn out and the only thing you can do is replace the whole pump unit. I made sure the fuel flow had no air coming to the pump and when I replaced the pump the engine ran perfect. If you install a new pump unit reset all of your settings on the needle at 2 turns out and the regulator screw flush with the housing then retune from there.

I hope this helps
Larry