Welcome to the board.
Agreed that it was a later replacement, but not so much on the placement. The V PTC's don't make much sense though because they'd go almost too wide to veer back in and up/down through the neck and into the nacelles. The only reason to have the V would be to attach to the deflection crystals, IMO. Perhaps aftward vertical branches would come off and head up... which would actually place the core further forward than I have done.
Glad I haven't set it in stone.
Regarding the swirling in the intermix shaft, I don't think we saw the Voyager's
swirls flow in a particular direction... they just swirled. It's possible that in the horizontal refit shaft the reason why power appears to pulse towards the nacelles is that antimatter is being injected into the shaft and reacting back up into the nacelles.