If I remember correctly the bottom rail was the factory return, no need to plug as it isn't used once the factory regulator has been removed and the rail end was cut off. I ended up returning the fuel to the factory filter/separator. Didn't want to gut the whole interior to return to the tank, no issues yet.

So your setup like the cool fuel?
New fuel pump, regulator and excess fuel pressure returns to filter

Close,I removed the mechanical pump on the seawater pump, relocated the fuel filter block to the front bulkhead, Aeromotive pump mounted low in the bilge pulls fuel through it,fuel enters 10micron filter mounted on the back of the rail. then exits out the front of the rail to a aeromotive adjustable efi regulator with factory vacume line hooked up to it.....fuel does not run through cooler. I never had a vapor lock issue, always problems with the vst tank assembly. Runs better than it ever has.

All good, but unless I again am misunderstanding, fuel should come from the tank, to the fuel filter, then thru the pump. Going thru the filter first is best to help save from crud entering the pump

Yes the merc filter /separator, which i think was a 40 micron, is before the pump then the 10 micron is before the rail/injectors