Let’s start with base camps. Most of the trailheads have some sort of parking area or campground associated with them. As I said before we used the Big Sandy opening most of the time but the Green River Lakes entrance is really nice because of the lake. The thing about this area is that when you plan on seeing a lot of the Windrivers, these campgrounds are someplace you leave from and then several days latter return to, like the guys in the linked video did. If we were hiking we would only use the camp grounds as a place to park the truck and then we would hike into some destination, like a lake, where we would set up a base camp. Then over several days we would fish and take short day hikes to other lakes or waterfalls. So I guess I would recommend looking at the maps and picking a spot that you think you can reach within the first day’s walk that looks interesting to you and make that your base camp. Or if you are traveling light, have several days to spend, and want to really see it all, you could start at Green River Lakes and have some other person meet you at a different trail head and drive you back to your vehicle at the GR Lakes. (ANY VOLUNTEERS OUT THERE?) Once you leave the parking/ camping area there will be no established campgrounds, you just pick a spot to pitch your tent and that is your campground. The Windrivers are huge so there are tons of places to see. They are a giant wilderness where you can go days without seeing another human being! In many places the trails will start out being nice wide dirt paths with bridges over creeks and then as you get further away from your car the trails slowly become a game trail and in some places will completely disappear so be sure to watch your landmarks and your maps it is easy to loose the trail up in the high lonesome.
I mentioned fly fishing because most of the lakes and streams you will see up there are full of fish. When we hiked we would always catch a few brook trout for meals and fly fishing usually catches a few. I have also used small “Mepps” spinners with good success. There are small game and birds in the winds too but you may need a license to harvest these, if you happen to see a forest ranger.

Several things to be aware of, which you probably already know. Elevation will make you short of breath and can cause problems due to altitude sickness. Sunburn is easy to get. Be sure you drink lots of water!! In the spring and early summer the mosquitoes can be horrendous so netting or sprays are a must. If they are real bad you may have to set up a camp away from water and out of the trees where the wind will blow. This is bear, lion and now wolf country so stay aware and carry a side arm. Keep a clean camp to avoid temping them with food smells. When you are near any water be on the lookout for moose. If you get close to a cow with a calf you risk being stomped to death. In fact the same can be said for all of the moms and babies up there. (It always amazes me that so many people go into the woods and think that these animals are tame.)
Always tell someone where you will be, what your route is, and how long you will be away. Then be sure to call them as soon as you are out of the woods and done hiking. Again the winds are isolated and if you get hurt you may never see a rescuer. Will you have any sort of GPS with you?
It sounds like you are very experienced with this sort of thing so I do not mean to “talk down to you”.
I wish I was going with you! I am sure you will love the area.