Ooof. That's rough. I agree with Blink- don't get demoralized! You can still win even with a heavily mutated character. Keep at it! ANd congrats for getting that far! Now get there again!
It should be easier now that you've managed to get that far once.
Here's a few things I noticed while parsing over your dump.
1) You're still overtraining spellcasting. I'd have rather had more fighting, dodging, or conjurations over 27 spellcasting. Other skills might have been good too. Also, when you want to avoid bad miscast effects, you should put more training into the spell schools of the particular spell over more spellcasting. Spellcasting might give you small improvements, sure, but I'd rather get the increase in survivability sooner than later.
2) You don't need two level 9 spells. Even having one for a three rune game is debatable. ...now, I still make a beeline for firestorm when I'm playing DE casters, but I usually plan to tackle at least some extended. Or maybe I don't, but I go for them anyway because they're fun. Doesn't make that the best choice though- they're costly and very very loud. You can tackle a three rune game very efficiently with an elemental bolt like bolt of fire and a reliable backup for monsters that resist it- iron shot, poison arrow, and orb of destruction are favorites. (not all three at once, though, you don't need that much)
3) I don't suggest quaffing regular !mut unless you've got a good way to take off bad mutations, like a !curemut surplus. !benemut is fine, but be prepared for the possibility of wild magic. (which is a mutation I love, but you have to be flexible with your playstyle if you get it)
4) There's some other strategies to avoid mutations: do your damnedest to avoid getting mutagenic glow, break LOS to mutating creatures (neqoxecs, cacodemons, shining eyes, orbs of fire) until you're up next to them (especially when you lack rMut).