Very good, we are making progress I think. It appears that the CPU commands are not reaching the VFO PLL. Since the CPU separately drives the VFD display, this would explain all the symptoms you are seeing. We have a good idea of what the problem is ... we just need to locate where the problem is :)
Note: I say "appear" because there is a small possibility the decoder/counter IC on the VFO board is fried and holding the lines up/down. More on that below ...
Next is to check the interconnects: the FT-980 VFO PCB (like most of Yeasu's PCBs in that era) is a single-sided design. These types of boards have known long-term reliability issues with solder joints due to the uneven flexing that occurs as they heat & cool. Additionally, the boards are neither temperature-stabilized nor fibre-reinforced, which exacerbates the issue.
Going to the CPU board, can you check the equivalent pins on that side (J6003 & J6013 I believe):
Outcome 1: If you see the correct signals there, we know we have an interconnect problem.
Outcome 2: If you don't see the signals, we need to eliminate the possibility of a fried VFO IC: disconnect the bus between the boards and retest. I
Outcome 2A: f we have a bad VFO IC the signals should "magically" start working.
Outcome 2B: If they do not, it would appear to point point to a CPU board issue. We'll cross that bridge if it comes to that.
Give these next set of tests a try and we should hopefully figure out where the issue is!
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-Mat Breton, N8TWn
Mat Breton N8TW