Hey, better late than never!

I have some projects that have been open/in-a-fix for years now.
The point is you got it done and possibly learned something new.

Quite possible... or at least when loaded down with the CPU it might not be 12.8V. IDK, it's a strange design indeed with the Compaq/HP PSUs, but I do recall seeing a few of them back in HP DC5000 SFF computers and similar.
Well, PFC (be it APFC or PPFC) doesn't actually increase the efficiency of the PSU. If anything, it decreases the efficiency. In the case of APFC, heat from the APFC MOSFETs, diode, and inductor are essentially those losses. And in PPFC, it's heat generated in the PPFC choke/inductor's core and windings.
However, PFC does reduce the reactive power from the PSU, which in turn may make the delivery from the power co. to your house a little less lossy (though that depends.) So if you consider just the PC/PSU as one system, PFC decreases efficiency. But if you consider the PC/PSU + power co. delivery system as one, overall that may increase the efficiency or at least increase stability in the system (highly inductive or capacitative loads... i.e. loads with high reactive power... can be problematic for the power company.) So all in all, it's probably worthwhile to keep it.
Anyways, congrats on the repair!

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