I remember reading somewhere he had Seymour Duncan do a custom wind for that guitar, but it would be good to verify that. Otherwise, I would also suggest the Abraxas pickups, which I understand to be a bit of a misnomer anyway since they don't seem to specifically target his Abraxas period. Those are nice clips you posted, I'm a big fan of early/mid Santana too.
As for the Yamaha SG, I have 2 but can't seem to bond with them. Too thin necks for my taste...