The B and C sections are mostly RC coupled (for B, one is, one isn't) and if you change the cap values there, then the tone of those stages supplied by B and C will change. I would leave those alone.
I would also leave the bias cap where it is now. Going too large increases the time constant at that stage and it can make the bias too slow to react to changes which you do not want. 100uF is about as large as you would want there.
For section A, it was carefully designed back in the day by Dynaco for hi-fi and essentially copied by Sunn for MI use. Caps were also expensive back then so they used the smallest cap that would get the performance they were looking for. Caps are much cheaper today. That said, as PRR noted the C L C filter in there with the two caps and choke in between is designed to work a certain way and changing any of the values changes its performance. The higher cap values are only appropriate to use if you are going to use solid state rectifiers. If you plan to use tube rectifiers, then the values of the cap at the section before the choke must be reduced to below 60uF, and with today's poor quality GZ34's going lower than that is a good idea too. The early Sunn 2000S's used the dual GZ34's and Dynaco transformers. Then they changed to Schumacher transformers with a slightly higher B+, and dual GZ34's. Then later they got rid of the GZ34's and used solid state diodes from the factory. They never changed the filter values, but caps were still expensive and the performance was fine for the day so that likely explains why they never redesigned the cap values.
Using larger caps at node A before and after the choke will give a bit tighter and more present bass. I know of quite a few Sunn 2000S's that have this mod and they are perfectly reliable with it. The owners seem to like the increased and tighter bass response. I wouldn't do the mod if I was using guitar with the amp but it works fine and sounds good for bass.
Why do you feel you need to make changes to it if it is and has been working fine with the modded cap values? You can leave it as is or go back to stock as the others are suggesting but I wouldn't go larger in cap values at the A node than what it is now. If it was me I would leave it where it is as I like the feel of the tighter/quicker bass response, and it is perfectly reliable with those values, but its your amp and your time so do what you want to it.
Greg