I think you should definitely talk to the project owners first. It's a nice offer but I'm sure they will want to know what environment their ads are being shown in.
You could try setting up a Meta question (including a link to your site) and asking those who put up the ads to leave a message whether they want their ad being shown or not.
Another thing to be aware of, using the SO iframe might cause confusion on the SO end when views and clicks are analyzed, so you should talk to the management as well.
Maybe talking to individual ad owners and copy+pasting their banners (bypassing SO's mechanisms entirely) is the best way, albeit the most bothersome for you.