Sounds like you had a pretty real intro to sheep hunting!
Glad you guys survived not much worse for wear and it seems like you have a great mindset re: getting tuned up for the next round.
Some thoughts in response to your well thought out analysis.
Food - I use three ultralight stuff sacks, one for breakfast, one for lunch, and one for dinner to keep food organized and things easy to find. Generally I am not a fan of stuff sacks, but these weigh less than ounce each, basically nothing, and are a big help when packing and unpacking your bag etc.
I can't fathom carrying around a jar of peanut butter or bag of torts on a sheep hunt! I find it very helpful to lay out my breakfasts, lunches, and dinners by day to make sure I am not overdoing it on food, which I almost always do. I also weigh everything at the end to make sure I am within that 1.5-2lbs of food per day target.
Rain Gear - The heavier duty stuff will do a better job at keeping you dry, but the trade off is that it is...heavier and less packable. As others have noted, rubber will leave you just as wet and it sucks to carry. I use the Sitka Stormfront set and have been reasonable happy with it. If you get caught in sideways rain and 100% humidity for any length of time, and you do on most sheep hunts, you get wet regardless of your choice of outerwear.
I wash my Goretex gear in Nikwax Techwash and then treat it with Nikwax TX direct about once a season. The TX direct replaces the DWR coating which helps the outerfabric not wet out...for a while. The Tekwash cleans the whole garment including the waterproof breathable membrane, which is the most important bit when it comes to staying dry.
Boots - Try some more mainstream mountaineering brands like Scarpa and La Sportiva if you have not. Zamberlan, Mammut, and Lowa are worth a look as well. You will eventually find something that fits your foot well and that you don't have to spend crazy money on a custom fit which, in my experience, is just as likely to fit poorly as anything else. Make sure you get a lot of miles on them before your hunt. Even with good fit, there is some breaking in of the boot and your foot that needs to happen each year.
Tents - I switched from a Nallo 2 GT to Anjan 2 GT as my sheep tent a handful of years ago and have been very happy with the weight savings. You do give up a bit of stability and durability with the lighter fabric and poles in the Anjan, but so far it has stood up to some pretty rough weather. Proper staking and guying is key with all tents, but especially the Hille's. The big vesti is key during long sits in crappy weather, keeping packs dry, etc..
Knees - The downhill with weight on your back is what tends to really crush your knees. In my experience, the best thing you can do for them is hike up and down hills with a pack on your back. Start with light or no weight and then ramp it up to 45-50lbs as you get closer to sheep season. Starting slowly and building up and being consistent with your hikes and training seems to do a much better job of conditioning uphill and downhill muscles than just jumping in with heavy weight. On my first few pack hikes of the season, my knees and quads always feel like crap. Sore, achy, weak, etc. After a handful of hikes and starting to ramp the weight up, they feel much better.
It takes a while to get your mountain legs under you and if your training doesn't mirror the conditions you actually face on your hunt, you are underprepared and things will hurt. Based on your "no brakes" analogy, I'd said your quads and downhill resistance muscles are the issue, not bad knees. Your knees hurt because the muscles supporting them weren't strong enough to do their job well. Very, very, very common. The buddy I helped support over the last few days on his first attempt at getting into sheep country had the exact same experience. He had been hiking to get in shape, but nothing mirror the grades we were on in the mountains. His legs were in full failure mode, ala "no brakes" on the way down. If you done a good job of preparing and don't have any underlying or previous injuries, eventually you should only feel a bit of light muscular soreness and little no joint pain. Ben's recommendations are solid and would be great additions to the uphill/downhill game.
Again well done on the character building experience and bonus kudos for packing a brown bear out as part of the sufferfest. More kudos for the reflection and after action review. Seems like you are on the right track!
Best of luck.