Ok, Did you plug the thermactor system holes on the back of the heads? when the system was removed? I assume you did.
I would not eliminate the EGR, It doesn't give you much if any performance improvement. But it does lower combustion chamber temps(Nox) while it's functioning. Just do the checks I posted to find your egr problem(Usually a pretty cheap code to fix).
As for the 41 & 91, I am doubtful of the o2's causing this. With one new one and one unknown aged one it just doesn't make sense. If it was the 1 O2 sensor you would get either a 41 or a 91 depending on what side the o2 failed on. You are getting a 41 & 91 which means both banks(Both Sides) are Lean!
When you put the new Pump in, Did you also do an adjustable Fuel Pressure Regulator? Did you set this right(Vac Unplugged)???? Set to about 37-38 with vac unplugged?
Only things that can cause this are lack of fuel, or to much air(Intake gasket Leak-Can find quickly with brake clean or something sprayed around gaskets. Listen for Idle change or stumbling). Unless your exhaust pipes are blowing black smoke and stink of fuel(Rich) Like Need mentioned, then I would doubt the O2's imo.
Ummmm.... It's Black, Shiney And Did I Already say Black?