Set in an old dormitory school in England...
Um, Hogwart's is in Scotland, but we'll let that pass.
Obnoxious, stuck-up, blonde-headed British rival whose first name starts with "D"...
The idea of an obnoxious stuck-up rival hardly began with YSH. This is a staple of many many stories of teenage and late childhood angst.
Two boys and one girl sneak out of their rooms at night to investigate strange goings-on...
Again, a staple of a particular genre of fiction that both YSH and the HP books are referencing.
Friendly school teacher turns out to be in league with dark forces...
Again, a staple of fiction.
Deaths occur through the use of exotic potions/drugs/spells...
Once again, a staple of fiction.
Chris Columbus involved in a key creative role...
And don't a lot of us wish he wasn't.
Kids journey via unlikely flying contraption...
The point where I nearly threw something at the screen in YSH. I think these points are getting increasingly tenuous.
Shots of kids eating inside a hall at long dining tables...
EH?
Clever girl, comic doofus, & brave talented protagonist make up central heroic trio...
Again, a staple of fiction, and Ron is not a comic doofus - that role is Neville's (though given Columbus's level of directing skills, Ron did become a very flat character in the first two movies).
Mortal arch-enemy survives to fight another day...
Again, a staple of fiction.
In short, case not proven. The links are all staples of fiction that YSH, HP and a vast number of other movies all draw upon. You also missed out lonely childhood of the central characters (again, a staple).
Rowling's stories hark back to the first golden age of children's literature (arguably we are in the second at the moment), when many of the books had the following characteristics:
(a) Central character who is either orphaned or separated from adult control.
(b) A humdrum life is transformed by discovery of another world where they are to play a pivotal role.
(c) Because they are naive of the new world, they must learn all about it, and in doing so, are transformed.
(d) Typically, the character must save the new world from destruction and in the process identify and destroy the source of evil. Often, there will be the need to uncover evil in innocent guise.
(e) At the end of the story, the character has gained inner strength and awareness and their personalities changed from positive to negative.
Any of this sound familiar? It's been the ubiquitous plot for nearly every classic children's tale (and some real lemons as well). Psychoanalytic theorists argue that it is an attempt to help children cope with the transition through puberty into adulthood, learning who should be trusted when you, rather than your parents have to make the decisions, etc.