I did 3 years in A-7E's (VA-82) frpm 84-87, so I may be able to help.
1) Yes, those ductings were on both sides, they are wave guides for the radar and avionics. To my knowledge, there weren't any re-manufuactured E's from A's and B's. All of the E's were staight off the line as E's.
2) The antenna's on the intake were on all E's, the A-7's that look like E's that didn't have then are C's I beleive. All the E's I saw in 84 had them. A A-7C was basically a E with a TF-30 engine.
3) The Chaff buckets where on the bottom side, just aft of the tail hook frm the beginning. Same location