they will not be 100% but I have been running beta with 3.5 stuff including the ap's and I have done 0 conversion other then give clerics channel. So yeah they will run fine.
I'm trying to figure out if the previously released items like Pathfinder Adventure Path, Pathfinder Modules, Pathfinder Chronicles etc, are completely backwards compatable with the new Pathfinder RPG or if they are going to be redone.
Pathfinder RPG is designed with the goal of backwards compatibility.
I've run Rise of the Runelords with a mix of 3.5 rules, PFRPG Alpha rules, and house rules, and am Running Curse of the Crimson Throne with Beta rules, and it's quite doable on the fly, with only minor tweaks - it's a quick and dirty method, to be sure, but it's not that dirty. A bit smudgy, perhaps. Definetly not filthy.
So Adventure Paths work well enough. Modules should be the same. The other stuff (Chronicles and Companions) are usually on the rules light side and should work even better. The Pathfinder Chronicles Campiagn Setting, for example, is easily 90% flavour, and the 10% rules mechanics that are in there are easy enough to convert.