I recently had my 500 EFI,s full total rebuilds , new everything ,I ran them for a little bit without shutting off ran amazing ,I took boat home to flush then they wouldn't start up only on the little gas that was in line , so first thing I thought out of gas ,put 15 gals in still wouldn't run just fired over for a split second , so then I went and filled boat completely up and only took 60gals so I know there were 50gals aboard ,brought boat home then fired right up ,I can run them all day and run great as long as I don't shut them off ,when I do they seem like they only run on whatever gas is left in line , I can hear the fuel pumps coming on ,but they just seem to run out of gas , took the boat out yesterday and rode it for a good 40 mins ran amazing ,shut it down and took an hour or so lunch , came back to boat both of them fired right up ,then port seemed like it ran out of gas ,but starboard stayed running and got me home ,along the way I tried numerous times to start the port but just would only fire over for a second and seemed like no gas ,took boat home to flush port fired right up then,,im guessing Im not pulling gas up to my pumps , any solutions to this before I drag the boat all the way back to the shop ,hoping there is something I can do ,

did the fuel filters get replaced during the rebuilds?

Yes ,They are brand new also ,

Sounds like vapor locking to me. Port engines generally vapor lock easier since the fuel filter and return are near the headers on both engines.
Ethanol fuel also vapor locks easier than ethanol free.

Yep, vapor lock. Bring along a rag and baggie. Next time it does it, remove cap off shrader valve and put rag next to it. Then press in on valve until you get the air out. Fire it up and put the rag in the baggie

Thanks for the feedback , that sure makes sense to me , is there any suggestions for a permanent fix ???? I was told to run 87 pump gas is that ok???

Your current setup sends unused fuel back to the fuel filter. The fix is to reroute the return line back to the fuel tank. If you not getting any codes from Knock, I would say 87 is fine, but others should know more then I about the 500 requirements.

The fix is......throw the cool fuel in the trash and install a bypass return regulator and a electric EFI fuel pump,