Question 1: Formats does not directly address this. I can tell you that I do not use continuation number on transposed material from volume to volume. So if volume 1 is print pages 1-c35 and 840-a840 volume 2 might be d35-b61 and 840-a840. As you can see, I WOULD use continuation numbers on the "regular" text. Just not on the transposed material. This is an agency decision however and should be handled consistently throughout the whole transcription (whichever way you do it).
Formats does address the idea of continuation letters in the Table of Contents. According to 2.10.7a, continuation letters are NOT used in the Contents.
Question 2: These types of materials would only be placed in volume 1. The exceptions to what would be included in volumes other than volume 1 are things like pronunciation keys and cast of characters in a play that is more than one volume.