I found a few new things in the desert and involving recruits from the desert. As well as some scenes I finally managed to get.
1. Sunny doesn't vanish if you refuse her or let her join (and you can do the event again) nor does the picture...leave/return and the chrystal is back. So you can't get the chest.
2. Ask Sunny to do something and you get a blank Yes/No prompt; answering Yes gets her to hunt for food as usual.
3. If you build Alice's house, the scene from earlier when you first found Doll Castle with Marisa plays, and Reimu ends up stuck in the trees (I had to Town Portal out of there). You can also walk on the trees there, but it doesn't help when your character is still scripted to move downward and you need to move up.
4. Entering Marisa's from Alice's rebuilt house also reverts back to the Forest Dungeon portal. Like the earlier glitch, leaving and returning from the direction of Kourindo/Forest Entrance fixes this.
5. Youmu's crystal comes back and you can re-recruit her.
6. If you ask Youmu to work, she says she got /[v](number gained) food, probably something to do with the variable formula being shown.
7. Asking Nitori or Kogasa to work at the item shop without someone else there makes them double up and leaves a dummy in the second shop place.
8. Yoshika, Merlin and Rin also stay behind when you finish their talk in the pyramid, and you can do the event again.
9. The skeletons in the tomb's bottom floor don't vanish after killing them.
10. I can't find Rin or Merlin on the map since I didn't have room for them in my village.
Characters you can't evict for any reason
Option doesn't do anything: Lily White, Kogasa, Orange, Mystia and Sunny
Option doesn't work: Nitori, Yoshika. In the former's case, she is still in the house and reappears where you would have normally found her if not recruited, while the latter gets a prompt to evict Star Sapphire instead and she stays in the house
Characters not equipping what they should
Wool Hakama: Reimu
Wool Dress: Marisa, Alice
Not sure if the above is supposed to be like that or they're just not implemented yet so I'm mentioning it just in case.