I have the LP and the CD. You're right: There are two cuts on the LP -- "In a Mellotone" and "Summertime" -- that don't appear on the CD. Likewise, there are five cuts on the CD that aren't on the LP. Also, each format features different track sequencing. It's a jumble!
That said, I think both the AQ and sequencing are preferable on the CD. As an album, the CD just works better.
As for Shirley Scott organ playing on the Live at Rick's LP: I think that's mistake in Discogs. OTOH, I haven't heard the LP in a while, and my memory isn't what it used to be.
Hmm. I'm not familiar with Truly Wonderful. . . . Might need to look into that.