As a fellow Michelangeli fanatic I must warn you that unfortunately his recorded legacy can be a bit of a mess. As you know he had a very small repertoire, playing the same pieces most of his life, and it's not always entirely clear which CD has a studio recording, which one is a good quality live recording and which one a bootleg. You must also ask yourself how many different recordings of the same piece you want to have - one, two, all of them? In some cases the way he played a piece changed enough over the years to say there are several important interpretations, but in other cases his crazy perfectionism makes it difficult (for me at least) to tell different versions apart.
So... here are some recordings not in the two boxes that I believe are wonderful enough to check out:
BBC Legends: Scarlatti, Beethoven, Clementi, Chopin
1961/1959 radio performances. This includes the final Beethoven sonata which I don't think is in either box, and what I believe is the greatest performance of Chopin's second sonata.
BBC legends: Beethoven, Debussy, Ravel
Two Beethoven sonatas and a Debussy encore from 1982, with an unbelievable Gaspard de la nuit from 1959.
(These two BBC CDs are also part of a 3-CD edition called "Portrait of a Legend" which includes the Grieg concerto from 1965 and Debussy's Preludes I from 1982.)
Decca: Beethoven, Scarlatti, Galuppi
Studio recording of the Beethoven sonata mentioned above.
The Vatican recordings - this used to be a 4 CD box of pieces you mostly have, but played live in Vatican City. The June 13 1987 Gaspard de la nuit is very interesting, quite different from the way he played it in the 50s, but great as well. You find that same performance here.
Aura: 10 CD box - Not sure if I should recommend this, because these are for a large part the same recordings as in the Warner box, but it's cheap and there are a few things you may not know yet like the seven Scarlatti sonatas.