502 Mag MPI with cool fuel (non VST) system. Intuitively, I would think that the "out" arrow from the fuel filter head should be plumbed to the inlet of the fuel pump, and the line from the pressure regulator goes back to the "in" arrow port on the fuel filter head. Is this correct?

The boat I'm working on is reversed. The line from the fuel tank goes to an "in" arrow port on the fuel filter head, but then the "out" port is connected to the regulator, and the other "in" port is connected to the fuel pump.

At best, I'm thinking that this is running the filter in the wrong direction, potentially decreasing its efficiency? At worst, more load on the fuel pump or even reduced fuel delivery under load?

Your correct the Reg and pump is swapped

Doubtful, in’s/out same size and paper flows same both ways. but the fuel pick up in the water separator is the threaded nipple the filters spins on to attach. I would guess prming woukd be difficult and lot more chances of vapor lock without having a lower fuel pick up in the separator. Think of separator as a fuel reservoir.

Now, if system has low psi pump feeding separator, this would not be much of an issue as it’s keeping separator (reservoir to high psi pump) full.

hopefully explained that okay ?

No pump feeding separator.

As I think about it further, chances are the fuel isn't even being filtered. The pump is drawing from the same side of the filter as the tank is supplying it. it's basically bypassing the media entirely.

Going to put new filter elements on and then swap the lines.

Thanks for the input.

yeh, if from tank line is on same side as element to hpressure pump, you are right.

and if that’s the case i’d be checking injectors screens and the screen in cool fuel just under regulator. Look at microfuce, have to temove reg from cool fuel and will be right there,

inlet arrow: from tank
other inlet arrow: return fuel
outlet arrow: to high ores sure pump
other outlet arrow: pipe plugged

I thought in factory form the to and from lines to the pump had different size fittings at the fuel filter head ?? goof proof.......thats the way I remember my 502 mpi's were....IDK been a few boats a go........

Maybe. I'll take a closer look... they appeared interchangeable at a casual glance.

In addition, these 502s have MEFI 1 PCMs and the early MPI Keihin style injectors, but have the later cool fuel system instead of a VST. So it's possible someone bastardized the whole thing at some point over the years.

They are

mine were gen 6 mefi 3's