I think you will find that the M3 sends a program change message to the JV when you load the combi. Try using EX2 and set the Bank Select to some bank that the JV doesn't use (check the JV manuals for bank MSB/LSB settings).

The CZ-5000 was my first synth. The sequencer is the bomb. Unlike so many sequencers, even in DAWs, in step mode each track can have it's own length so it's possible to create all kinds of fun polymetric behavior. I once set up a song with each track length based on prime numbers...7 bars, then 11, ...

Novation web page here

Novation web page for Circuit Tracks

All you need is a MIDI OUT jack on the 88 key instrument and a MIDI IN on the 61 key instrument. They both look like this: https://images.squarespace-cdn.com/content/v1/58976aeee6f2e12da0026d7f/1557498179754-2FW35BN2KP50JOTSAANA/ke17ZwdGBToddI8pDm48kHJeHSC8xWw2nROrSL5Z47dZw-zPPgdn4jUwVcJE1ZvWEtT5uBS...

I'm an EE very familiar with software so I also wonder how the OS ROM could cause the problem, but as you stated, the old ROMs exhibit no issues. So it's the only thing that's changed, right? I'd look for release notes for the various OSes and see if anything comes up as a red flag. BTW is this a VF...

What was the source of the new OS ROMs? That would be my first thought, that the ROMs are corrupted somehow.

Do you have schematics? I'd focus on the ROM that holds the PCM waves (too obvious?).

You probably already know the drill...open it up and check the cables interconnecting the various boards.

Do programs and combis switch OK from external MIDI messages?

From p. 73 of the Operation Manual: Timbre Parameters MIDI page Status This controls the status of MIDI and the internal tone generator for each Timbre. Normally, if you’re playing an internal Program, this should be set to INT. If the status is set to Off, EXT, or EX2, that internal sounds will not...

If what you want to do is record parameter changes, during recording it should just record any CCs being sent. If what you want to do is what people call automation these days that can be done in real time by setting the recording mode to be overdub. In Session mode, youy can set a clip to loop in o...

You need to check all the internal power voltages first. With your symptoms, bad power is the most common cause.

I then did a factory reset, which got the machine running, but shortly after that it wouldn't come back on. Does "it wouldn't come back on" mean that nothing lights up or shows on the LCD or do you mean something else? I'd take a close look at the power supply voltages. Do you have the factory wall...

Anything could have been used. A lot of what was used was just whatever was available cheap. Money talks ;) Linns still weren't cheap in the late 80s. Jupiter 8...well only if someone was really lucky, they weren't selling for $200 like Junos were because not as many were made and their original own...

In this thread from 2015 there is some discussion of Prodigy features, serial numbers and dates.