Enzo and particularly Phil, thank you so much! I had figured that something like Phil's analysis would apply, but I never actually had to anatomize such a circuit before and needed some guidance. Right...
I applied contact cleaner to a 1/4" plug and worked it in and out of both inputs, then did a partial reassembly on the workbench. Amp to speaker, amp to reverb tank, jacks back in speaker chassis. I kind of hoped that would sort things out, but actually the problem is worse than before. The jacks are really noisy, and wiggling the plug creates lots of full-volume speaker abuse. I think this is because the sub-board on which they're mounted has been shaken up so much over the last few days.
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I think I have to go ahead and disconnect the sub-board from the main amp board, install a new input jack, and make Joe's switch-mounted-in-spare-jack-hole thing work.
It will take me 24hrs to fully digest Phil's breakdown (like a python swallowing a goat). But it sounds to me like I can put a DPDT switch into the unused jack drilling, and use it to route the signal from the guitar to either 1&4 or 2&3 on Phil's diagram (which may or may not be labelled that way in real life, but we'll cross that bridge when we come to it). I'm concerned that I may be omitting to earth something somewhere!
In answer to Phil's question: "Hey nifty a Q, are you saying that the Od input and the Boost Switch are on that PCB? If so then my wire numbers I mentioned earlier are wrong." -- I'll do my best to give a straight answer. The 1*3" PCB sub-board that appears on my first gutshots carries both input jacks, a five-cable ribbon, and separate black and white leads to the overdrive footswitch. The five cables in the ribbon *must* correspond to the inputs in your diagram, surely, and they're numbered 1,2,3,4,5 where they join the main board. The time I spent with the multimeter and trying to work out the PCB gave me the distinct impression that those number assignments are different from those in the schematic (remember this is a Supercube 100, not the Cube 60 from the schemo). I think they're just reversed. I can presumably confirm that by tracking where the connections go to on the main board. Give me time.
One small point from my previous note that didn't get answered. If I'm joining the cables from that five-way ribbon connector to the new DPDT, I will need either to pare them apart with a craft knife (messy) or lug them into some kind of breakout board. Any recommendations?
Best NP