Are you finally deciding on removing the the original BOSS stepper controls and replace them newer drivers? If so, then yes, you can remove almost all of the electronics, especially the 3x saturable core reactors. There are a number of power supplies in the original design and they all have bridge rectifiers in them that you can reuse if you are going to use DC stepper drivers. You can even reuse one of the transformers for your DC power supply with a little rework of the coils. However, you might as well just buy a toroid transformer (much smaller and easier to package) and make your own DC power supply. I always prefer to find drivers with an AC power input because you do not have to mess with the DC supply. However those are more expensive drivers. Are you going to keep your machine on 3 phase or gut it and switch to single phase and add a VFD? I like my machine on 3 phase with the original drives because it just keeps on chugging away and will rapid over 150 ipm all day long. However this is almost pointless for my hobby only use.
Do you know what drives you want to use and what their maximum DC voltage is? The large T2 3 phase transformer has taps for 60-70-80 VAC and you can just use one of the coils for the power supply. I believe the secondary windings are about 2V (?) per turn so if you unwrap a few turns, you can reduce the voltage enough for it to be safe for use with Gecko drives after it is rectified. Are you keeping the original BOSS motors?
I think I may have posted my schematics on here before. You can probably search for it.
Did you ever get one axis to work on Linux with the original phase drive?