I've pretty much figured out or confirmed the pin outs. These color codes are refering to the 12x10 SEF coil and not the Tornado.
1 (brown) & 2 (grey) is to the transmit coil and I'm pretty sure based on my readings that those wires are hitched up properly and that the Xmit coil is within specs. I took a reading on my 10" Tornado coil to compare ohm readings and both coils at pins 1 & 2 read 1.9 ohms.
For pins 4 (Reciever Coil Output, Brown) and 3 (Ground, Yellow) I got 1.218K Ohms for the 12x10 and 1.119K Ohms for the 10" Tornado, so I'd assume that's hitched up properly and that the RX coil circuit (see explaination below) looks to be OK.
I checked online and managed to find some general TX/RX info on Sovereign coil windings and the above numbers for both coils seem to be within specs. Really the RX coil reading isn't of the RX coil, but rather a general reading of the resistance of the entire circuit on that end because of the pre-amp and other components involved in that the RX coil alone can't be isolated unless you cut into the coil (see above schematic).
Pin 5 (No color since not used) is for sure the VDI output signal to the meter via the meter's cable from the control box. Since this signal isn't needed in the coil's cable this pin isn't used. That signal only takes place between the meter and the control box, obviously.
Here's where things are still a little dicey for me. What I can dig up shows pins #3 and #6 to be common grounds to each other. You can even see that referenced in the above hand written schematic. However, when I checked my 10" Tornado coil with an ohm meter it didn't show any connection between those two pins. Only #3 shows to be the ground. Fine, but then why am I seeing solder on pin 6 of this SEF coil's connector? Either the SEF requires something to be done with pin 6, or perhaps somebody made the mistake of hitching a wire up to that pin and then changed it.
As I've said, there is a tiny little black wire inside the cable as well that isn't hitched up to anything on the plug. I've attempted to check that wire for conductivity between it and pin #3 (to see if it indeed was a common ground tied to 3 at the pre-amp and thus meant for pin 6) and I'm not seeing anything continuuity here so they don't appear to be common grounds that are tied together. In fact, I'm not even sure if this little guy is even a wire. I need to look at it under a loop because by eye it looks like this tiny little black "wire" has a white fuzzy material inside it and not wire. Just need to sort this last bit out.
In summary, though...I'm pretty sure 6 isn't used for anything, that black "wire" isn't meant to be a wire (unless maybe it's a ground shield meant for the external connector case?), and that this plug's pin outs are all properly in place. Only thing left to do is wait for some input, but by then I'll probably already have powered this thing up and confirmed that there is a problem. Which comes first is based on how much patience I have.
What's also confusing is that some of the old material I've come acrossed says the pin 6 is used on certain coils, others say it's not, and so on.
Incidently, while digging through some dark deep corners of the web I came acrossed a cool little article on double D coil designs with some very interesting information about their traits. I'll try to post a link to that.
While I'm at it, I also came acrossed a blurb about some of the older aftermarket coils (CoilTecks maybe, or perhaps the initial Excellerator round coils?) not having a pre-amp on the RX coil. Somebody remarked that he was planning on putting an external pre-amp inline on the coil cable himself, and a much better one than what is currently in the coils that do have it (higher sensitivity, less noise, less target degradiation). That's a project I might be into experimenting with, since I didn't see any further remarks on progress being made. Something similar in a way to the external pre-amp Shaun's amp is using on the TX circuit, though on the RX coil this time to amplify the RX signal and not increase the field strength generated at the TX coil. I'd just need to figure out which older coils out there don't have a pre-amp. Anybody have a clue? I would figure they'd be rather poor performers, and that's why I'm thinking of the original round Excelerator coils from years ago?