A couple of observations, your hull should have a knee wall about 14 inches high around the motor well , at the back of the cockpit, right?
I don't know the correct terminology, but I think what I
call a "splash board" is what you refer to as a knee board.
I made one since the boat didn't come with one. It's
around 20" high I think. Water doesn't come over it, but
it definitely seeps through at the bottom. The floor of
the splash well is not completely flat so there may be
a 1/4" gap. I plan to get some weather stripping to make
a better seal or make another splash board that won't
have as much of a gap.
Do you dunk your motor pretty good when drifting in a chop?
I don't believe that the motor gets dunk pretty good, but
I think a decent amount of water is coming in the splash
well which results in a decent amount of water, for my
liking, seeping under the splash board. Once it seeps
under, there is another rear rectangle hatch that leads
to...shoot I don't know boat terms...the gallows.

( it
is where the bilge pumps are), then the water goes in
there. Another thought of mine is to make that hatch
water tight.
You have floor drains in the back of your cockpit correct?
Does water flow in from them when at rest or when there is a little chop action going on while drifting?
Yes, I do have those drains. I believe those are called
"scuppers" as mentioned in another post? I had to
google what scuppers are.

I'm thinking that some
water might flow in when there is a bunch of water
that has seep into the gallows

. I've seen the drains
not draining at all due to all the water that has made
it's way down below deck. At that point, I have both
bilge pumps going and I move forward towards the bow.
When you get out of the water on the trailer and you pull the garber plug how much water comes out?
Assuming you have not capsized it on that trip? ;D
There's not a lot of water because I'm on top of turning
on the bilge pumps often.
Where does that bait well drain to? I am assuming you have a hose or pump at that drain on the floor, right?
I have a connecting hose that goes to the bottom pvc
elbow. In turn. that hose goes through a hole I drilled
at the bottom of the splash well. There is a gap in that
hole, so that is something I can improve on.
You are talking about two footers and being only the second V I have ever heard of getting capsized, that is very serious and I would hate to see you or someone else for that matter get hurt. Let us know.
I'm sure when my boat capsized, that it was a gradual
event. With their 35 gal bait tank back there and at least
one adult, I'm sure water slowed filled up below.
Here are more images of the bait tank as promised: