Ahoy Ragamuffin,
You'll want to look closely at the portlights that are available and buy the best your budget will allow. I've found the ones that most closely approximate original equipment are made by Lewmar . . . and they're probably the best made of the lot. We've never had a gasket or weatherseal come off a Lewmar and the company stands behind their products. Look in the West Marine catalog online (westmarine.com) or cruise one of their stores. I think there may be one Lewmar size that's an exact (or almost) replacement.
If you're going to add portlights, remember there's an air gap between the liner and the trunk cabin shell. Once you've made your cutout, fill the gap with a bead of silicone all around to stiffen the liner. It'll help you not compress the liner hard against the shell and, downstream, should the seal between frame and cabin side fail, you won't have so much free water show up in some strange place inside the boat. Good luck with your project!