The thing that really is confusing me is the fact i unplug the FPR that the pressure does not go up?!?!?!
What do you mean "unplug the FPR"? The FPR is a fairly basic back pressure regulator, there really isn't anything to unplug. Maybe you are referring to the vacuum line, but that isn't going to affect fuel pressure when it's not generating adequate pressure to begin with.
I'm not sure why you have low vacuum, but I wouldn't be too surprised if the low vacuum is a symptom of it running rough because of low fuel pressure. I'm not sure at this point that the vacuum reading is diagnostic.
Perhaps a quick, basic description of the fuel system is in order. The fuel pump supplies fuel to the fuel rail with the FPR closed. Pressure builds up in the system until the design pressure is reached, at which point the FPR opens and allows the "excess" flow to return to the fuel tank.
Basically, with fuel pressure readings like you are seeing, there are two possibilities: either the FPR is opening too soon, or there is something wrong upstream of the fuel rail that is preventing pressure from building. So, the next step in diagnosis, is to determine which scenario it is.
Changing the relay checked the relay, but obviously the relay isn't the only component in the fuel pump circuit. Is there any other sign of a loose connection or voltage drop in the fuel pump circuit? What do you get if you put a volt meter on the fuel pump connector just behind the tank (ground the fuel pump test lead and you should see a steady +12V)? If the fuel pump isn't getting a good electrical supply, it may not be able to generate the necessary pressure.
Have you determined if any fuel is getting past the FPR? Some use a pair of vise grips or similar to clamp off the return line somewhere and see what that does to the pressure (if the pressure jumps up, then the FPR is likely opening too soon). I've gone so far as to disconnect the return line at the FPR, run the pump, and see if fuel is getting past the FPR. Where you've tried replacing the FPR with a suspected good FPR, I'm not sure the FPR is at fault here, but it's prudent to check.
The problem, I expect, is going to be somewhere from the pump to the rail. You said you've changed the filter, so maybe we can assume the filter is good. Is there any sign of clogging, kinking, or other restriction in the supply line?
You said the fuel pump is relatively new, and we all hate to change a part that we hope is still good. One case I've heard of is the pump itself is good, but the little rubber hose that goes from the pump to the top of the tank either leaks or otherwise doesn't seal, so the pressure is bleeding off right in the tank. I personally would check as many things outside the tank as I could think of before dropping the tank.
