What are you calling the area that you step 3 inches down into when you go
into the cuddy area, the superstructure?

No. I misunderstood your description.

I thought you wre taking water into the cuddy from the foredeck.

The superstructure on a vessel in anything built above ("super") the deck. If
you have
a raised enclosure around a cuddy cabin rather than a spot you simply crawl
into
unto the foredeck, that raised enclosure is superstructure.

You could call the cockpit sole a "deck" as it is an exterior surface, but
since the cockpit sole is on a different level, etc, than the foredeck and
sidedecks (if any)
using a more specific word or phrase serves to minimize confusion.

Lots of times you'll hear that surface described as the "cockpit floor", and
while not all that nautical it certainly works for me.

Sounds like you could have some water caught in a section between frames and
stringer in the forward bilge. Maybe.
Two things to investigate: how is the water getting aboard in the first place?
And, did the builder put in a limberhole that has become plugged up?