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1) I throw out most of the cosmology and replace it with Planescape. Pharasma is a borderline overgoddess (she's been pushing at it on a multiversal time scale, but she's not quite there), and the "Golarion sphere" is a bunch of different spheres all pushed up close to one another, with decaying sphere walls (the decay has a reason, but none of the campaigns have quite figured it out yet), all in a cluster.
I have had a similar idea. Basically, Golarion's multiverse exists long before the D&D multiverse. At some time in the future, something happens and The Boneyard - already connected to the various planes via portals - becomes the Lady of Pain's prison (the Lady of Pain being Pharasma, obviously).