1. Don't know for sure. Can't think of any difference, although the seat foam is specific to standard or custom
2. I recall from discussions long ago that the thicker custom panels need a different regulator with a longer shaft, the Custom panels have a door pull and they have different door latch handles. Other than that, someone who has done it needs to comment.
3. Unless the repro upholstery material has changed in the past few years, none have the original "breathable" Comfortweave of the '68 Custom Interior. Some repros have a close look pressed solid material pattern that resembles Comfortweave. I don't know which repro is best. Several years ago you could still find the original Comfortweave material at
https://smsautofabrics.com/ and have upholstery made to match the original.