Hi Nathan,
Now that you've decided to cut your hatch covers by hand (good choice by the way) here's a tip that you may consider.
It has been my experience that using a thin kerf Japanese pull saw to cut hatches can actually leave too thin of a kerf. In order to completely seal both the edge of the cover and the deck against water damage, you'll need to build up the thickness of the epoxy to some degree. The thin kerf left behind with a Japanese pull saw usually doesn't leave enough room for an adequate buildup and still allow enough wiggle room for the hatch cover to fit back in place. One way around this problem is to double scratch your cut line. Using a pair of exacto blades taped together with perhaps a thin shim between them will yield a pair of cut lines that are perfectly spaced. All you need to do is keep the saw blade between the lines and then once you've completed the cut, simply sand back to the lines - you'll have a perfectly sized gap between the cover and the deck. This technique also allows you to be a little sloppy with your cut yet still end up with a perfectly shaped opening and hatch cover.
Note that you'll need to make a hatch cover cutout template out of something a bit stiffer than paper - poster board works well and gives the scratch tool a fence to ride against.
Also
Joe

: Thank you all for your helpful responses. I think I will make the cut by hand
: with a small japanese hand saw or similiar. It is a daunting thought,
: cutting a hole in this thing, but I suppose no more daunting than
: everything else so far - it has been such an amazing learning experience
: for me. I almost feel I got in a little over my head with this project,
: the cool thing is that it has forced me to finish it. I'm looking to
: finish it in the next few weeks, I'm about 13 months into it so far. I
: attempted to input a picture, if that doesn't work there is a link below
: to a photo. Thanks everyone.