Power to pin 85 comes from the ECM relay output (pin 87)so if you don't have power at pin 85 and you're jumpering power to the fuel pump that would be telling me that it's not an ECM issue, but an issue with the wiring from the ECM relay to pin 85 or that the female socket that the fuel pump relay plugs into is bad (broken wire, dirty corroded female receptacles)

Is it safe to assume that you have the 310 page gt40 manual?

What you're doing obviously works for you and you could keep doing it but it's not the safest thing to do.

If you have your jumper in and the boat quits for some reason like a fire with a burned through fuel line feeding the fire, you have to manage to get to the jumper and remove it or the pump just keeps feeding gas to the fire.

The factory wiring in conjunction with the ECM automatically turns off the fuel pumps if the engine isn't running (if the engine quits with the key in Run for example, the ECM takes away the ground for the fuel pumps and they stop) I think it's a USCG safety requirement that the pump automatically shut off with the engine not running. Same thing with cars that have electric fuel pumps, the government says they have to shut off automatically. 

Since nobody replied to your post from yesterday about this same issue, you can delete it to avoid confusion. 

If somebody replies, then you can't delete it.

Which leads back to the question of do you have the 310 page manual?

You can figure out lots of  stuff with it, like what color wires go to which relays   

If you click on the link below, you'll have it

http://correctcraftfan.com/downloads/PCM_GT-40_Service_Manual.pdf" rel="nofollow - link

There are quite a few discrepancies but it's better than not having one at all

In that post, follow the Green arrow in the picture, click on Post Options and you'll see a dropdown with delete post as an option......click on that and it's gone.

That option doesn't show up if there's a post after yours in the thread.

I was getting ready to begin my "no-start" checklist I put together and ran into a problem right away with the 8-Pin connector on the back of the engine and need advice how to proceed. 

It seems that I am missing a pin on the male side of the 8-pin connector...or, maybe it's not supposed to be there in the first place. My guess is that the orange wire is supposed to combine with the red wire on this side of the plug and has something to do with alternator charging the battery.

Do you know if these connectors are still available for purchase or something equivalent?

Kinda a repeat of earlier, your pumps not running with the STO jumpered stil tells me that you don't have a computer issue and that the problem is the wire from the ECM 87 to FP 85.   Your diagrams and readings seem to back this up

I'd do some untaping of the harness and run a new wire and/or replace the FP relay socket.

And........check your PM's 

I think you need to read the link below to a thread on Planet Nautique and find the diode he's talking about and replace it. (he has basically the same thread here on CCF, but the pictures disappeared from the CCF thread)

The pictures he has are real helpful for location and the explanation is really good too.

The diode is in the  wire hooked to the "I" terminal, so if you do your bypass, it's basically doing the same thing without a diode.

I'd give it a shot and assuming it works, get a diode like in the link and put that in (or now that you should be able to see the pictures in the link, find the diode and replace it)

Pictures along with some words are a wonderful thing

Like your last picture for example......if your assist relay is wired the way you describe, then it's not wired right.

Here's an earlier picture of yours that only shows one wire on the "S" terminal but other connections had me wondering if the wiring to the starter was right.

Here's a PCM diagram to look at. 

One thing to keep in mind is that 28 year old faded purple wire can look pretty brown

And a hand drawn version from a 2000 gt40 engine, no Brown wires but faded, discolored Purple

And you put up some good diode and splice pictures too