RE Quick Ben and the dragon(s) fight: The original poster might sleep easier with this bit knowing that another partial reason for QB being able to beat them is given in the first chapter of the Crippled God, in particular regarding Menandore. But it is also down to what others have said already:
- Obsolescence is one of the great big themes of the Malazan series. Ancient powerful deities chronically underestimating the powers of the present world they find themselves in. Times have moved on. What was once considered insanely powerful is not anymore. Dejim Nebrahl in the Bonehunters being the perfect example - in the end, they didn't need the Deragoth to take care of him, as Paran mused afterwards. And you see this in several other instances throughout the series, including QB's fight with the sisters.
- Intelligence and trickery: If you notice, QB doesn't take them head on straight away, wave of magical power vs. wave of magical power. He uses the environment and the sisters themselves against each other. In the end, they beat each other - QB doesn't kill any of them himself.
Some of your other questions:
- Brys' resurrection: As another poster pointed out, Hood's influence is not present on Lether, so everyone lingers after death. Blood and flesh also seemt ot be very much part of resurrection magic, thus the fingers and body. When the Guardian said he would have a companion and took up Brys' body at the end of MT, I don't think he meant he'd just have a silent rag-doll body to talk to!
- Toc: My favourite character...so it's good to know that dead doesn't necessarily mean dead and gone in SE's world, eh?

- Jaghut on the Ice Throne: I don't think you have to read on and find out, I think enough hints are given during that sequence itself for you to jump to the (correct) conclusion that that is indeed Hood's body sitting on the throne. Which finally confirmed the suspicion throughout the earlier novels (green hands, Jaghut ghost faces before character dies), that Hood was a Jaghut.
- Tool's return to mortality: This is easily skipped, because it's never directly said in MoI, but from asides by Silverfox and Tool's throwing down of his sword symbolism, the interpretation is that Silverfox really does have the power to return true life to the T'lan Imass...but most of them, after hundreds of thousands of years, would choose oblivion, methinks.
- Rautos Hivanar and Taxilian: Both fried/crushed during that bit at the end with Icarium's machine going wonky. But dead doesn't necessarily mean.......
