Had a little delay, due to weather, illness, and my wife having surgery, but did a little more on it today.
Trimmed the filon flush with the metal frame on the aft hatch. I had to use a non-bearinged laminate trim bit, as the ones with bearings had too big of a gap between the cutting surface and the bearing. I used my cheap speed saw instead of my nice beg router and it worked great.
Started to install the trim but it appears to be too small. Looks like I will order the next size up.
I also caulked around the exposed edges of the plywood inset with Dicor non-sagging Lap Sealant. Now I need to find the screws and re-install the hardware.