Dude, you closed up too soon.
First, don't mess with cutting anything down there. It is NOT a good idea.
The C30 Association website and/or the Google or Yahoo Group will tell you why.
The most important work that you MUST do is to simply stop letting anything but stuffing box water into your bilge. You already know you need to stop the portlight leaks.
Companionway?: get a piece of Sunbrella and cover it, or buy a dodger.
Shower drain? Way old design, shower stuff does NOT belong in the bilge. Tons of C30 skippers have installed the Tupperware solution, either hand made or purchased as a kit from WM. Peggie Hall mentions shower "crap" in the bilge as one of the nastiest things going. It is potentially unhealthy, and just plain stupid, but you do have an old boat. Even Catalina stopped doing that, finally, my '86 C34 has a shower sump with a dedicated diaphragm pump, check valve and vented loop.
Ice box drain? Cap it off and pump it out into the sink. You're losing "cold" by having a hole in the bottom of the box.
A/C condensate? I don't think you ever bothered to mention the maker of your A/C. I don't have A/C, but I've read so much about this issue over the years that while I have no cause to doubt you, it's gotta be the very first time I have ever heard that a vendor wouldn't allow it and would void the warranty. Please tell us more.
Closed? How are we to help you? Why?
I do understand posting in two different areas of the site. But I sure wish people would simply get in the habit of looking for posts by using the New (Legacy) feature, so one could see ALL the posts. Never know what you could learn.
Hope you get your knickers out of their twist, and can begin to address your issues.
Good luck, most of the folks actually tried to be helpful.