Just found this original trailer for Baby It's You on IMDb and, if the songs present in the trailer are any indication of the songs on the original theatrical soundtrack, there's quite a bit missing on the video.
John Sayles does not detail the missing ones in Sayles on Sayles, but here is what I noted from the trailer that I don't recall on the DVD:
*"Shout" - The Isley Brothers (listed in the End Credits, but "Surfin' Bird" plays in the scene that " Shout" appears to have originally belonged to)
*another Spector-ish song sung by a female vocalist, which I couldn't name
*"Hurt So Bad" - Little Anthony and the Imperials
Of course, the songs in the trailer are not a definite indicator of the songs that appeared on the original soundtrack of the film. The only way to be sure of what has been changed would be to obtain a television/cable dub of the film (which contained the original soundtrack), catch a 35mm (or 16mm) film screening, or obtain an original press kit, which most likely lists the full credits for the film as they originally appeared.
On a final note, I initially thought that the version of "Baby It's You" that plays in the film was a cover, but on a second listen, I believe it is the original Shirelles version.