Couple of thoughts:
1) Are you running a thermostat? Or, did you drill some holes in it? ECOdiesels are notorious for running hotish. Not sure why. If you are running no t-stat or have drilled holes in it, or it's stuck open, you might be affecting the mileage due to lack of thermal efficiency. Others can chime in, cause I really don't know much about it. But, the bottom line is you want your diesel to run in the 190F range (87 C).If you aren't in that range, it can affect mileage.
2) Have you checked that your fuel return line is clear to the tank? One of the trouble-shooting tips is to blow the fuel back to tank and make sure it's clear. If not, that can affect mileage.
3) Compression test? Some think that off compressions can affect mileage. I'm sure it can to some degree, but I'm not sure it can account for 15 MPG worth of discrepancy. But, it could be a good idea to check and rule it out. But, given the mileage you were getting before this happened (see below), I'm not sure this is the problem. I just can't see a sudden drop in compression causing this (even if you blew the HG, which I'm sure you'd know, unless of course there's no T-stat in there.
The 40-43 you were getting with the stock AVX trans and stock injectors, is about right for an ECOdiesel. By dropping the RPMs with the 3.94 final drive, you should have improved it. That means the following:
1) Assuming your T-stat is working properly, and has no auxilary holes in it, AND, your fuel return line is not clogged, AND your compression is decent, then the only logical conclusion is that your pump needs a rebuild. Increasing the internal pressure will address only ONE part of the equation. It will not compensate or fix other internal pump problems like worn/broken components, worn springs, sticking components, tired delivery valves, misadjustment, etc.
I'd say, have it rebuilt. Or, better yet, have a true TD pump rebuilt. The stock ECO pump has a smaller pump shaft, and lacks the LDA. Really no point in bothering with it if you want performance and power.