While it is doable, the Charge controller has copper plate on top and bottom of the PCB so more unnecessary work leaving the NC legs on, personal preference perhaps.

You could make a daughterboard "capacitor pcb" that fits the original holes. Or a redesign of the pcb, I could do that for the first version if you want. Wiseguy designed the last version that I can't modify. But you might have the boards allready?
It's a robust design made for long life so better do it first time right.

I think I'll have a go at drilling the PCB with a template. My PCBs will be a part of a bulk order, so can't be individualised.  Likely will solder the NC connectors as well for support, since these are 90mm high. Also I will only need 6 if I'm correct.

My haul of choke candidates: Two small and one big, from an Aerosharp. Three small of comparable size to the small Aerosharp ones, one from a scrapyard of comparable dimensions to the large Aerosharp, and two from the Aurora of dimensions 106x52mm outside, width 45mm, centre hole 73x20mm.

Are the Aurora ones candidates, being substantially bigger than those sourced from Aerosharp? Any suggestions for installation?

The 5Kw Aurura choke, leave that one together it is practically good to go for the Charge controller, the 2 coils can be joined but the polarity needs to be checked with the an LCR Meter, forgot what the numbers are, you can find that out later.