Sorry for the slow reply, I don't check in here that often these days.
Just to move this discussion forward one step...
The first step is to get as grounded a view (or analysis) of the tune as possible.
What I would do would be to look at the analysis of the progression from a combination of functional harmony, historical tune analysis, and law of resolving tendencies all at once.
The A section is in D, and the progression goes to the traditional/typical IV chord (G) in the 5th bar.
The rest of the A section is a cliche: G (IV/D) | G-(IV-/D) | F#7 (III7/D) | B7 (VI7/D) | E7 (II7/D) | A7 V7/D) |
EXCEPT, the last chord is a deceptive cadence, resolving to D- instead DM.
Now, backing up a little, starting with Bbo7: The| Bbo7 | A- | D7 | G | can be seen as a progression in G.
Dim7 chords can have a number of functions. One of them I think of like this:
Remember Scott Joplin Maple Leaf Rag? it has a Dim7 chord resolving to a Maj chord on the same root. In G, this would be Go7 -> G Maj. That's what is happening here, but the Go is over a Bb root for voice leading purposes.
The parent scale of the Go7 might be considered to be G Diminished, but I think an even more consonant choice would be G Lydian Diminished [G A Bb C# D E F#] (this is often a great choice for a Io7 in-first-inversion chord in a very tonal progression). Either could be used, but point being, we are in G Lydian Chromatic.
Back to the "Joplin progression", what if we delayed the resolution of Go7 -> G by putting a D7 in between them? Go7 -> D7 -> G.
If we look at this from a Law of Resolving tendencies point of view, we do a very basic shift of G Lyd -> C lyd (one step flat lying) -> G Lyd (resolving by moving in a sharp direction).
This D7 is then broken down into a ii-V by making it A-7 D7.
So, my A section vertical analysis looks like this:
|D I | G LD I | C VI | C II | G I | Bb VI | G LD VII | C LD VII | D VI DII | Ab II Bb LD VII | F VI F II |
The Law of Resolving Tendencies can clarify some of the choices. For example, the A7 -> D- at the end of the A section can be analyzed in many different ways. However, because D- is clearly F Lydian, I chose Bb Lyd Dim VII for the A7 because Bb Lydian resolves so nicely to F Lydian.
we can now place these on the cycle of 5ths chart:
Ab Eb Bb F C G D A E B F# C#
Argh, that's not really looking correct when posted, but you get the idea.
There is reharm stuff in the older book. Alternate chords can be based on the original analysis, informed by the Resolving Tendencies of the new progression, bass/root movement, melodic movement, and voice leading.
P.S. edit the next day: I was just playing through this tune and I was reminded how many choices there are, while at the same time the Bossa style makes my choices more tonal than other jazz tunes might. Today I liked the Lyd/Lyd Dim II interpretation of F#7 and B7.