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I'm pretty sure Keith plays an acoustic in open E for Prodigal Son and then switches to a resonator (which sounds quite poor imo) tuned to open C for You Gotta Move. There's photos out there of him playing both at the MSG show so i'm pretty sure that's what he did. It also just sounds like two completely different guitars.
If I remember correctly, Bill Wyman wrote that Keith's acoustic were poorly tuned at that times. I tend to think the same and understand why the tracks added in the 2009 YaYa reissue were not in the original release.