All,
If I was a betting man (and I've been known to wager a bit here and there) I'd place money on the problem being with Q27, a uPD8255AC-5 programmable I/O controller. This takes muxed CPU data and drives a number of subassemblies in the rig, among them the VFO and PLL.
One of these ICs went bad in an FT-980 and caused the tuning to simply not work (among other problems). Replacing it fixed the issue. Yaesu must have foreseen potential troubles in this portion of the CPU Unit, as Q25-Q27 are socketed.
73 - Fred, N8YX