Running out of fuel

I have an 07.5 lmm that has a duel fueler kit, 15% over injectors, water methanol injection, fass lift pump, larger tank pick up tube, self ported fuel rail fitting(7/64 hole), shimmed pop off valve, and over 200,000 miles on it now. Order it the way I wanted it, now I'm really loving it!
I have had the banks big boss kit on it after I hit 60,000 miles. Then ended up buying EFI live. Now I stack the 2 just to keep the safety's for the transmission since it's stock. The truck has been great except since I installed the injectors(fuel pump went out), my fuel rail runs up to about 24,000 psi on a wot run. It never reached the 26,000 desired pressure. I see my frp command climb all the way up, or down in percentage. My first thought was the rail running out of fuel, so I ported the fuel fitting on the driver side. I am still having this issue. I tried going back to stock torque numbers, and still have the issue. It does seem to run a little longer now before the change fuel filter come on, but it still happens. I make all my test runs without the banks on, I can't log any data with it in the system.
I'm not sure how I can be running out of fuel with 2 pumps and 15% over injectors. My fuel rail command goes from 48% down to 12%. Also I don't think it's the pop off, as it doesn't drop instantly and it's not shooting too high. It's a gradual increase up to about 14-18,000 psi and then never catches the desired pressure. It's just 1-2000 psi under. Am I missing something? I'm not sure where to go from here. Any help would be greatly appreciated!!!