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So I haven't Played D&D since when the Ebberon setting was first released.

I purchased the Pathfinder PDF books recently and like what I see.

Am I right in assuming that the Pathfinder rules are compatible with those Ebberon books?

With a little tweaking, yes. It is still essentially 3.5 with some modifications. The stuff that changed wouldn't change the campaign setting, like grappling rules.