Trying it out, and it's quite good! Nice work.
Let me share my impressions and thoughts. Of course I realize this is your personal mod, so feel free to disregard, but in case you're interested in feedback...:
The Good* The biggest improvement for me is the casting timeout. This means higher level spells are more important and you can't just rapidfire a weak spell into a massive burst of damage. It's precisely what I'd always thought was needed.
Truth be told, it should be even longer, to account for spells being more powerful. Game's a bit too easy now.
* The improved sneak and backstabbing is great. I'd never seen much of a point to the rogue in the original game, but this mod is a whole another story.
* Wand damage is now lower than cast damage. I like it, as it makes dedicated caster classes better at what they do compared to others. (even if it means the Earthsmite Wand in Q2M3 stops being my Favourite Drop Ever).
I'd love to see the above things go into the official version of the game.
* Armor penalty to stealth makes sense.
The Less Clearly Good
* Push/Repel: I liked how a few fast casts could push melee enemies away so you could then fire a damage spell safely, but with casting timeout it becomes harder to use them to create space. If you do increase casting timeout more (would be a good idea iMO) this technique might become unreliable against fast targets like Priam's guards or Shadows. Perhaps give those spells more oomph? With a corresponding increase to mana cost.
* Armor penalty to magic may have been unnecessary. Priest is meant to wear chainmail as he doesn't get Mage shielding spells, and Paladin and Knight already start with a weaker Magic stat and lower mana regen. Mage is going to get huge damage mitigation from shield spells (and rings) and yet won't suffer penalties from that...
There's also the added incentive to remove armor before doing pre-combat or non-combat casting (buffing up, Knocking on a secret door etc.), which would be annoying. Almost tempted to autohotkey it despite the cheese.
I'd recommend reverting this change OR making it impossible to change armor except in town.
* Armor penalty to speed I'm not so sure about either, at least from leather. One mildly absurd consequence is that strictly speaking, the optimal thing to do immediately after creating a Mage character is to undress him. That's just silly. The chainmail/platemail penalties make some sense, though.
* Wand class restrictions - Knock was a staple wand on most of my characters, and it's annoying how much harder it can sometimes be to get into some locked secret areas. I also miss being able to use Earth Bind on melee characters, to bring down fliers. Overall not a fan of this change. If cast damage being stronger than wands was on purpose, then dedicated casters from a given branch of magic will still have the advantage over wand users even if this restriction were lifted.
* "level scaling for spells and spell casting rates" - if this means what I think it means, namely that level (or magic stat) directly increases damage and decreases timeout, then won't this make the game too easy on higher levels? As well as reduce the value of the more difficult spells. Timeout is too short as it is! EDIT: yep, my level 10+ mage is ridiculous.

Level/magic already increased damage output indirectly, by allowing more powerful spells with less fizzling. And of course by giving you more mana to play with. That seemed enough to me without complicating it further. One magic dart should be like another.
Questions:Is there a comprehensive changelog available anywhere? (Yes, I saw the other thread). With more detailed/numerical changes/formulas used?
In particular, I am wondering about things like...
* How much is the sneak attack damage bonus? How about the flanking one?
* Heartrate: how much faster is mana regen at lowest heartrate compared to vanilla game? Is there a way to see what my current heartrate is? How long does it take to go to lowest heartrate once you end combat and stop moving?
* Is there a keyboard shortcut for the steal/unlock functionality? Browsing some other thread I run into some comment that there is, but I can't find it; I discovered mouse3 does it, but nothing on the keyboard.
* Rebalancing wands: was this just adding class restrictions, or did you change something about the costs/damage/mechanics?
* And lastly,
- made it harder to be detected while sneaking
What do you mean by "while sneaking" exactly, the "slower movement" modifier? Does running make it impossible to sneak altogether, or just adds a penalty or what?