The purpose of the FPR is to maintain constant fuel pressure across the injectors, which means it senses the manifold vacuum/pressure and through the vacuum line that attaches to the FPR it then compensates for any variation. Everybody checks to make sure that fuel pressure tracks with boost, which is important. But equally important is that the fuel pressure also track during vacuum or non boost conditions. Most people miss this important measurement, so you're not alone. So what you have described is that your FPR is not regulating during the vacuum part of the regulation. As an example, if the base fuel pressure is 40 psi with the hose unhooked, and if the motor idles at 18 inches of vacuum, then when you hook up the vacuum hose to the FPR, the fuel pressure should drop to 31 psi.
So here is what you do....remove the vacuum hose from the FPR, then adjust your FPR all the way down in fuel pressure and note this value. I'm guessing that this value will be about 38 psi. Then, whatever the minimum fuel pressure you can get, add 10 psi to it. So you get 38psi + 10psi = 48psi. Adjust your base fuel pressure to this new higher value and see how well the FPR regulates the fuel pressure. I personally have to run 55psi base because the fuel pump I'm using is overwhelming the stock fuel system. Most people run the 340 and it also can overwhelm the fuel system.
Wayne