If your pcm is setting ses codes, make sure that doesn't have anything to do with it. i've seen trucks run ok with 45psi, no bucking or surging, so that shouldn't be a big issue, it's not good, but it shouldn't buck with 45psi.
Since your truck had a swap, i bet the o2's were changed or are going bad, or were sitting around a while. When the pcm senses a rich or lean condition it will over compensate the other way.

If you have access to some kind of logging, check to make sure your O2's aren't stuck at zero and are not floating around 400mv's. A good O2 will toggle from +-50 to 900+ mv's, up and down like a nice sinewave.

Your fuel pressure doesn't look good either, if you currently have an intake pump, get yourself a walbro 255 pump, it'll work.

Good luck,
allen