Here's the glitch with #2

You're going to stain the wood etc. etc.

but it will get darker with the epoxy on it or... once the wood gets wet wether it's stained or not.
So, you have to guess how dark the stained wood should be considering its going to get darker when wet. As Rob said, you have have to do a series of experiments with some duplicate wood. Then save a batch of the stain or take notes as to how many coats. Hopefully you remember what grit sandpaper you used on the boat, because thats essential. Finer grit-lighter wood / courser grit - darker wood.

I admire tenacity. good luck.