Do you have the deck and hull joined together ? Last year I met a guy who built a Guillemot L, and he cut the hatches prior to glassing the deck, I believe the deck and hull were not joined yet. After doing the fiberglassing and later on joining both deck and hull, the deck shape had changed slightly. With the new curve, the already cut hatches didn't fit correctly and were leaking, so he was using duct-tape to keep them in place during the trip.
I'm not an expert in kayaks (hey, I'm just finishing my first S&G), but you may want to probably get more opinions before bypassing steps, and make sure that the deck shape remains the same.

Hugo