The problem with filling in the side limber hole plates is that the whole piece was shaped differently from Electric Boat to Portsmouth plans. The EB side plates are more angular and straight up front, while the Portsmouth/Mare Island ones fitted snugger, for lack of a better word to the top of the circular hull section, following the curve of the hull better. This was perhaps because (as in Alden) EB and Portsmouth had different ways of constructing the pressure hull, one yard building a more circular pressure hull and the other slightly more ovoid from top to bottom. That's IF I read Alden right, and I may well not have.
If you just fill in and rescribe the kit plating, then you'll basically have an EB side plate with Portsmouth limber holes that won't look right. Nautilus Models has side plates that may work for you. I've not physically handled them, but they're listed on their website.
Robert