Well, I was going to wait until I tore things apart further to ask, but
I figured maybe someone would have an easy answer to save me some time.

Here's the punchline: When we use the head (a Groco Type K) and pump it
out, the waste comes out the holding tank vent line.

This seems impossible to me. First of all, the tank itself is empty and
regardless of which way I flip the Y valve the waste still comes out the
vent line, which is attached to a three inch screw in top, in the top of
the holding tank.

Here are some facts that may help: The water supply for the toilet is
the fresh water tank. The previous owners put a ball valve before the
head, when you turn it on, water comes in the toilet bowl, then you turn
it off/down while you pump out the bowl,etc, and leave it off until you
use the toilet again. Completely non-standard setup, I guess. I've been
working on other more important things, but this was going to be my
next, um job, sort of, but anyway the first thing I was going to try was
to open the seacock toilet waste valve. I haven't tried this yet though,
all this has been happening with that valve closed.

Also, waste slowly leaks from around the top of the tank, onto the top
of the tank either out of the vent line or from around the screw
fitting. Whenever I look there is a little puddle of waste on top of the
tank. Again this seems impossible. How does the waste even get there
when there seems to be none making into the tank and while there is
definitely none collecting in the tank itself. I'm very curious.

There are only three through hulls in the boat (H33), the raw water
intake for the Yanmar, the head discharge and the sink discharge. I
really don't want to haul out the boat to add one(budget problems).

So, um, guesses? solid answers? things I should check first? Directions
I should head to solve this?

Thanks!

Stephen