I figured out the problem. The microwave did indeed crush and abrade the thermostat wires, but it did more damage than what was near the t-stat end of the wire.
I opened the Danhard controller box, and even though it had been several days, the smell of burned insulation came out of the box. The thermostat wires were fused from the short, and the one going to the ground had gotten so hot that all the insulation had turned to ash and the stranded wire broke from the heat.
I did some continuity checks, and got continuity along along each wire, as expected. But I also had cross continuity across two of the wires as well, which made me think that the wires were fried elsewhere, too.
What confused me about the t-stat wiring was that SMB used stranded wire in a gray sheath at the Danhard controller box, but the t-stat end had solid wire in a brown sheath. And the color of the wires didn't match. Also, the t-stat wire disappeared into the wall under the dinette seat and I couldn't figure out how it was routed. Same with the t-stat end: It also disappeared into a wall.
I figured that the two types of wire had to be spliced together somewhere, but couldn't find the splice until I took the fridge/micro/evaporator cabinet most of the way apart. Searching around by feel in the hidden recesses behind the cabinet, I found a wad of electrical tape covering a bunch of butt connectors. It had just enough slack in it to see how the color of the wires was connected.
I snipped off the damaged wire, but had to leave it in place because I couldn't pull it out of the wall. I marked it as "Do Not Use - Damaged".
I replaced the wire with new 18-3 wire from Lowe's. Instead of trying to make the long run through the wall again, I just used about 5 ft of wire and took the shortest path possible to the controller box.
Here's a pic of the burned wires. I had pulled the fused sections apart while doing the continuity checks. I figure there was at least 12V and who knows how many amps running through these tiny wires to cook the wires. Must have been pretty substantial.
Best of all, the A/C works again!
And I'm also beginning to understand how SMB puts these things together!