I rough trimmed the port side root fairing, then ground the high spots away with a very coarse 125mm angle grinder disc, taking part of a fingertip with it ... ouch. There was a small area of delamination underneath where I pressed the layup against the belly skin against the wing to close the gap during curing, so I ground that away and added another layer of thick carbon. When that cures I'll move on to fixing the overlap joggle with the aft fairing.
The fairing is thicker and a whole lot stiffer than the original part, so I won't need as many screws to hold it on, which was one of the aims.