Jay,
I wish we all lived in the same town, at this point a couple of us would just come over to help you.
Ok some more thoughts.
You said -
12.1 volts from the ignition terminal to the ground on the controller.
That is a concern, you seem to have lost .5 or .6 volts, that is a classic voltage drop. Usually a drop of that much or more suggests there is a wiring problem. (Bad connector, bad wire, bad switch, corrosion, loose connector, etc.) If I read your statement correct, this is the wire that supply's power when you turn the key. If so try two things. 1) What happens if you just put a jumper wire from the positive side of battery to that post on the glow plug controller. (Give it a full 12.6 volts.) Does the controller work correctly? (The controller is sensitive to voltage.) 2) What happens when connected normally and someone else turns on the key to on, does the voltage drop any more? My concern is by the time you get out of the truck, walk around, and look at the voltage gauge the controller has shut off. So you see 12.1 volts but maybe when it was running for that 1-2 seconds it was even less. (Voltage drops generally are their worst when they are supplying power/loaded.) This would be a potential cause for the controller to not work correctly.
Second to your point, putting in new glow plug wiring harnesses takes out a lot of guess work. So if the above does not result in anything, I would replace them.
I know you said you had a falling out with Classic Diesel Designs, but in this case from what I have seen they offer the cleanest offering. So you can avoid them, but you may be bitting off your nose to spite your face. Most everything else I have seen offered is partial wiring with crimped connectors. Since this system is resistance sensitive, these are just crimp connectors, that leaves a lot of potential down the road for more issues. You can buy the IH harness but it is a little different and has some other wires in it, you just don't use them.
I did see this on e-bay, but I don't know anything about it. But it looks like a decent build quality.
<p dir="ltr" style="margin-top:0; margin-bottom:0; text-align:start;">7.3 idi glow plug harness. Condition is "New". Shipped with USPS Parcel Select Ground.</p> <br> <p dir="ltr" style="margin-top:0; margin-bottom:0; text-align:start;">This harness is for non turbo models. We also have one for...
www.ebay.com
Sorry this is still haunting you, stay on it, you will fix it. Plus you will be much better at fixing the glow plug system down the road when something else is going on. I get the impression like all of us, you like your truck, and it will be around for a while!