Holy crap, that Red Hood arc of "Batman: The Adventures Continue" really complicated things.
As for the rearranged order, a lot of it is due to the Mr Freeze and Nora kerfuffle.
She's dead in the aforementioned series. Which means a few things:
1.) In order to keep the "Batman Adventures" (2000s) comic run canon, I'll have to ignore the fact that while Mr Freeze's head was going to be found by "Wayne-Powers" in the original script - that one page was still cut from the story and thus the page itself can't be considered canon. So Victor found his way out of that somehow...
2.) Batman Adventures #15 ends with Nora searching for her husband in the arctic. I assume that didn't help her cure, the illness came back and it killed her; as we see her dead in the "White Christmas" story of the Holiday Special comic.
3.) Finally, Nora's dug up corpse is seen in Batman: The Adventures Continue, so it's the latest point of that whole storyline.
4.) Nothing in HQaB:TLL conflicts with the Nora ordeal. Mr. Freeze is just in a Arkham cell moping. I assume sometime after that he ended up in the custody of "Wayne-Powers" and they reconfigured him by the events of Batman Beyond.
And the Jason Todd Robin thing became complicated when Slade brought up 9/11 and the fact Tim Drake had finals he had to complete (which can occur in December of a school year.)
Phew. That was a rough one.