Is there a set of settings that will make loading less painful?

It depends on what you are planning to use this mod for. I for example use whitelist "1xN Nx1 2xN Nx2" with height and width limit set to 20 and area limit set to 40...basically allowing up to 2x20 chests, which loads pretty fast.

My pain is the initial load on applying the mod. I have let the initial load of the mod sit 3 hours, with no joy.
How do i set the settings before the load?
Of, can you set default settings to some rather minimal values for quick initial loading, and require them to be increased?

Oh, I hope you overexaggerate. Lowering the initial limits should be fine

no exaggeration. 3h. how do I set defaults smaller before loading?

You can't, it the default values has to be set in the mod directly