I spent the last couple of hours making small subtle bends to the chassis to get the front panel square, it looks pretty good now. The weight of the toroidal transformer bent the sheet metal, which is surprisingly soft.
I've tested all of the outputs under load, looked at the startup waveforms (well behaved on all outputs) and measured less than 0.5 mV of ripple on the outputs. I have yet to see if the USB works, but that's about the last thing left to test. I'm sort of at a loss about what that mystery winding does but I'll probably poke around until I figure it out. The cut wire is around 22-24 gauge. All of the connectors on the transformer windings have what seem to be reasonable voltages on them. I put a meter between the cut wire ends and saw 2.3 volts, which dropped to 2 volts when the variable outputs were loaded. I found a service manual for the 3303S online, I assume it's similar. That one has seven secondary windings, some with taps, so there's a lot going on.
The damaged spot in the winding is under the center of the handle brace, not the edges. The center is raised up a bit, there's no way the handle brace cut into the wire. Whatever happened, happened with the handle brace removed or the transformer out of the box entirely. Somebody did it on purpose.
All of the outputs run about 100 mV higher than the rated value, which is actually within spec for the box (the fixed outputs are only rated at +- 8%). Wondering if they did that on purpose to compensate for lead resistance.
After the discount from the seller for shipping damage I only paid around $90 for this unit. It still has some pretty strong "fresh paint" smell and the manual and cables are still in sealed plastic bags. I think it's worth a little extra effort.