@Tobias ***************
people HAVE gotten the 60 day visit thai family extension from a tourist visa entry on amnesty THEN applied for the in country 90 day Non-O visa.
It can be done that way because once you get the 60 day extension you're back on 'hard stamp' (real time) in your passport and can apply for the in country Non-O and then wait out the under consideration period.
GO to your immigration office (with your thai wife and your documents) and see if you can't apply for that 60 day extension.