Nice track, great playing all around.
Regarding intonation and the B3 - the back is off. At one point the camera zooms in to the "oiling instructions". These are not good signs (well, there is nothing wrong with the instructions, but normally you wouldn't see it). Obviously someone has been "in there" for some reason. B3's are old, and notoriously difficult beasts.
I actually think the upper manual is at fault - it seemed quite flat at the beginning of Joey D's solo, and at the end of the tune, it's noticeably out of tune with the vibes. The lower manual didn't bother me at all.