I would not worry about whether your handheld vacuum pump maintains vacuum when connected to port on the FPR, too many places you can get leakages that are not related to a problem in the FPR. If the diaphram is ruptured in the FPR, I am pretty sure you will see fuel spitting out of that vacuum port on the FPR when the engine is running.
Also depending on what Aeromotive FPR you have, " NOTE: THE REGULATOR WILL NOT HOLD FUEL PRESSURE ONCE THE FUEL PUMP SHUTS OFF." https://aeromotiveinc.com/wp-c...9/131-0109-0revH.pdf
My Aeromotive FPR does not hold pressure when I shut the pump off. Its not an issue and I see it as a safety feature with no high pressure fuel in the lines / injectors when the engine is not running. 
With the engine running does the fuel pressure change when the hose connected to vacuum port on the FPR is removed?
Is the line connected to the FPR vacuum port rigid plastic?
If that line and the others connected to the throttle are rigid plastic, they could very well be brittle or cracked with age / heat. Check each one and consider having those replaced.
Speed-Pro are now know as FAST. You could contact them to see if you can get the latest software / instructions.