ronvonhagen - I'd get the paint as good as you're gonna want it before replacing the badges, if only because it's a lot harder to work the paint once they're back on. The adhesive will stick fine to smooth paint, if that's what you're wondering (doesn't need a "tooth"/scuffed surface, etc.).
I DO think you should clean off whatever's on the surface first (Klasse, wax, etc.) with a good solvent like 3M's Adhesive Remover, Wurth Cleans-All, PrepSol, etc. Glue doesn't stick to products nearly as well as it sticks to bare paint, might not stick long at all.
Gee, no way to talk you out of rebadging? Haven't seen a car yet that I liked better WITH than WITHOUT.