I'm not sure how I missed this thread!
Sounds like you're on the right track as far as troubleshooting goes. First check the vacuum that the CP3 is capable of drawing. It should be greater than 10 inHg when you crank the engine with a gauge plugging the supply hose. You should also test the vacuum signal on the filter while the engine is running. If it is less than 2 inHg then you have a fuel system leak. Normal is around 5 inHg at WOT. It shouldn't be more than 7-8 inHg under heavy load. Common restrictions include the sock filter in the tank and pinched / kinked soft fuel lines. Common leak points include cracked fuel lines (soft or hard) or fuel filter assembly.
Next is to check the CP3's fuel pressure outlet. To test the CP3 you'll need a mechanical rail pressure gauge to verify the electric pressure sensor and a scan tool capable of both displaying the rail pressure and commanding the fuel rail pressure regulator. Crank with the engine warm and the FICM disconnected to ensure that the engine builds at least the 115 mPa required for the engine to start. The CP3 should be able to build 160 mPa of pressure with ease and actual rail pressure should match the commanded pressure fairly closely. If it doesn't, then you need to figure out where your fuel is going. Common reasons for the inability to build rail pressure include excessive injector return rates, stuck / inoperative fuel rail pressure regulator, improper fuel rail pressure sensor readings, leaky rail pressure relief valve or a worn CP3. With the engine only having this issue when warm I would be looking close at the rail pressure relief valve. The engine may not be able to build the full starting pressure at cranking speeds if the PRV starts passing when the engine is warm. Once the engine is started, the CP3 spins fast enough at idle to provide enough volume to overcome the leak. The final check is return rates - Which you've kind of done already in a round about way.
As for your next steps, I'd get your buddy to come back with his scan tool and verify that the fuel rail pressure sensor is accurate as compared to a mechanical gauge and then observe the rail pressure while cranking when the engine is hot to make sure it is building sufficient pressure while cranking to start the engine. If it isn't, my first recommendation would be the PRV. If that doesn't fix it up, then the CP3 itself would be my next suspicion.