Lift pump problem

Hey I got my transmission rebuilt on 03 LB7 so I decided to retune at a shop to play it safe for my ecm and my transmission. They were having trouble flashing the tune in and I guess because of all of my aftermarket stuff so they removed a few fuses to make it work. Now my lift pump is noticeably a lot quieter and I’m not sure if it was a result of that. I was talking to the tuner guy he said my trans shifts a little funny sometimes because he believes I have a fuel pressure problem. My injectors all read fine with the highest being 3.0 the rest are either closer to 0.0-1.0. Could he be right is my lift pump just giving out , or did he mess up with some fuses. I did buy this truck with all of this already installed so I am a little bit in the dark in what fuse is what as well. I just bought some new fuel filters as well to see if that would help.