It sounds like you have plenty of ideas even if you are not sure which one to go with. Have you considered trying to figure out how you want the story to end, then deciding which beginning will work best?

 

Have him show up in the deep roads? either darkspawn poison gets in his wand and fucks with it, or he gets attacked/helped by dwarves, or something.

 

Are you still looking for ideas? I have a few if you're intrested

 

If you're still thinking of doing this crossover story I have a couple of ideas.

1. If you want to stick closer to canon, have Harry come out of the eluvian from the Dalish origin story. That's how he can meet the soon-to-be Warden and Duncan. And Merrill too, who I personally love in DA2.

2. If you want to go further off, have Harry show up in the Korcari wilds, distracting Morrigan & Flemeth. Because they are otherwise occupied, Alistair & the Warden die at Ostagar, and Harry & Morrigan have to go through the plot without them.

With a darker, jaded Harry, maybe he's willing to Imperius people into becoming allies since they don't have the Grey Warden treaties to fall back on. Or maybe Flemeth convinces them to use the treaties with Harry claiming to be a new recruit who escaped Ostagar.

You could then really screw up the rest of the party. Maybe Leliana's terrfied because her vision showed her Alistair & the Warden dying due to Harry's appearance, so she thinks he's a herald of darkness to come-- and she either wants to try to redeem him (which could play with the tension she has with Morrigan) or she buggers off to the chantry, who then joins Loghain in wanting to put a stop to Harry & Morrigan. Maybe that's why Zevran gets hired to take them out. Maybe Sten refuses to work with them because as a Qunari he doesn't trust the two mages.

You could even use some of the NPCs instead to join Harry & Morrigan. Jowan is an obvious choice.

Regardless, if the blight ends up getting stopped due to the actions of a couple of apostates rather than the Grey Wardens, that could have great effect on DA 2's Mage v Templar conflict.

I hope you do decide to write a HP/DA crossover as the few I've come across have either been disappointing in concept or abandoned all too soon when they do start to work.