Here are my thoughts:
0) It doesn't bother me at all that the PCs start just like regular students. They do the usuall first semester stuff and slowly encounter the mysteries in the school. Later on they will have their moment to shine and show how special they are. In the end it is a preference. Do your players like to know from every event happening that they are the chosen ones?
1) Adding more combat in the AP know for not being combat heavy, lol. First, undead are not present at all in the first book, so very out of place. Also Teacher Ot disapearing and somehow implying he can rise undead to test the student seems really weird.
1b) I'd adivce strongly not taking stuff away form PCs in the very first combat. Thats also just hurting the ones not being able to cast spells for no good reason.
1c) The spells are just there to boost the non-casters a bit. I've read somewhere that DMs are skipping them entirely since it unneeded bookkeping. That would even increase when you change the cantrips in little insignificant ways.
2) Just a preference, but having NPCs pranking the PCs by STEALING their stuff would make them a hated character from the getgo. My Player love Chizire, he'd never steal from them.
3) Again, I prefer to have all students be welcoming and with few having reserves (like Ignaci and Noxolo). Who would be even jealous in having to fight undead on the school grounds haha