It's an amazing trip and I love that you are spending extra days on the trail. Here's a few suggestions on your itinerary but the main one is to stay flexible. Absolutely no reason you can't decide to change things up on any given day.
If you want to leave from Happy Isles, you can arrive the day before and likely switch your permit and stay overnight in the backpackers' camp. That's what I did.
The trail between Thousand Islands and Purple lake is pretty easy. I skipped Red's Meadow (except for the BLT from the diner) and camped at Deer Creek. Alternatively, if I had wanted a shower and a stay in civilization I would have skipped Deer Creek and camped at Purple Lake.
You're spending a number of days between MTR and Evolution Lake, then making a big jump to Deer Meadow, and then skipping Palisade Lake. The hike to Evolution is fairly mild, but it's a tough single day to Deer Meadow, which is not a particularly interesting area having burned several years ago. I was so amazed by Palisade Lake on the other hand that I stayed 2 nights. There's some nice camp sites at Big and Little Pete. Then's it's a good day's hike to Palisades.
After that your itinerary looks much like what I did. Have a great trip.