I can tell you what I did/plan to do, with the same boat. My big opening ports were very leaky, actually all my ports were leaky, so I had to at least remove them for re-bedding anyway.
For the small ports, I replaced them with SS ports from New Found Metals. They make a size that's more or less a drop in from what you already have. After 4 years, so far so good.
The big windows, I considered all options, but for now, I just extracted them, reinforced the frames with a layer of glass cloth and epoxy and re-installed with new bedding. I cruise Long Island Sound for now so I'm not too worried about boarding waves.
My current plan (subject to change) is to simply install some window boards for any offshore cruising. Basically you just make a frame, such that you can slide the boards in from the top, around each window. When offshore or if a blow is coming, but slide the boards into place over each window. You can lock them into place with a simple door lock or something similar.
Since you are already getting rid of your vinyl lining and replacing it, you have more options to re-engineer the whole thing. This is doubly true if you are also planning on repainting the cabin trunk. I looked into doing all of that but had bigger fish to fry at the time.
For replacing the whole thing, I would probably find the largest windows/opening ports I could find that will fit into the holes. In addition to New Found Metals, these guys have some cool products:
Marine Ventilation Products - Mariner's Hardware
Although I can't vouch for their quality their stuff does pass the eyeball test.
I would then use a dremel or something to grind away as much of the coring as possible from around the empty frames. Then get some marine grade plywood (or solid pieces) that is just thick enough to fit into the slot where the coring was. Cut the plywood into a frame for each new window then epoxy the plywood into place, with the edges sandwiched into the gap where the coring used to be. You will have to cut the wood into a few pieces so it will fit. Then build up the inside and outside of the assembly with cloth and epoxy, fare paint, install and bed the windows, etc. Piece of cake.