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Thanks all for the insightful inputs!

I did as suggested, scrapped old config and created a new one using Mesa CT with the suggested home settings.
All golden now! (I had been going around in circles before...).

Opto switches - I had not considered the scenario where the LED had deteriorated, considering now putting some good old fashioned limit switches in, and using the opto for homing only (they have great repeatability).

Now to make some chips - I have 3D printed prototype hardware for the ball screw mounts (using ASA with 100% infill), now to see if I can coax them to at least center drill the parts in aluminum, after squaring up with Z physically locked and taking very cautious lateral cuts.

Yes,  so as a starting value, your ~52 analog scale setting  and
FF1=1.0 is at least a reasonable starting point.
 

10 turns is about 10.4~" and my calculated is 10.47".
Encoder scale set to 960 is perfect.