I want to add Austria and Hungary to my mod, but I want a good city list.

Wolfshanze's list looks ideal to me, except for the fact that it has cities for both the Austrian and Hungarian kingdoms.

So what should I do?

Hmm... I wonder what cities were on the Austrian civ in Conquests.

What you should do? Hmm... that depends on what exactly you want to do.
If you want to add the Austro-Hungarian dual monarchy you can use Wolfshanzes list. Only thing I'd do is making it homogenous if it isn't already (I truly don't know as I haven't looked at it now). That means I would either use the original name of every city (means Bratislava not Pressburg for example) or decide for one language for all city names, propably german or hungarian (as this were the most important languages in the monarchy).
If you want to use Austria and Hungary as 2 seperate civs, I'd suggest to search for 2 mods that add Hungary and Austria and take the city list from there. You could use the city list of my Magyar mod for example (Magyars=Hungarians), it is quite comprehensive. I am pretty sure there is an Austria mod as well, don't know anything about its city list. I suggest to take care for using cities that are inside Austria today. During the monarchy lots of cities belonged to Austria that actually aren't austrian, just like Prague.

I'm thinking of taking individual cities from each monarchy from the dual kingdom.

Also, I usually translate the names of the cities into other language to work with multilingual mods. For example, in my Poland civ, when you play in English, you have Szczezin, but in German it's Stettin, and in Italian it's Stettino.