Rod, I don't think you'd have to dig out the floor for that hole.Doing what you mentioned is fine.
As for the deck floor,here's my opinion for what it's worth."Paint it".
I did my deck floor with gelcoat with a textured finish.I am not happy with it.It is very durable and very non skid,and looked great for the first year,but it's a bi-tch to clean and it stains easily.
Don't be afraid of paint.Several of the very expensive high end boats like Hinkley are Paint over gelcoat on the hulls.
The two part urethanes are extremely durable and fairly easy to apply.You can mix some non skid additive in the paint for a good footing.One of these days,I'm going to sand the gelcoat on the deck and paint over it.
The deck floor under my seats was rotted out,and some previous owner had drilled several large holes(1")into the stringers.
I cut out the deck to solid material and glassed in a couple of layers of 1708 cloth than some marine fir plywood and finished it off with more 1708 on the top.My deck was too shot to try and keep the original pattern,so I didn't have to worry about perfection in the finished glass.
All my hatches were rotted as well so I had to dig out the cores and replace them.After all was done I mixed up some cabosil with Gelcoat to a consistency of ketchup and rolled it on.
Try a long flexible coarse sawzall blade in your hand,or a long cheap serrated kitchen knife to cut out the foam around the tank.Don't foam the tank when you re install it,as the foam just holds moisture and can make the take corrode.
You have a nice place to work on it during the winter(all year where you live)Good luck,keep us posted.
Here's a couple before and after of my deck and hatches.
