TL;DR
By 3,5,6# (Kirkpatrick actually writes "3,5, or 6#" — the "or" making things much more clear) Kirkpatrick is saying that sometimes only the third above the bass is included (3), sometimes a complete root position chord appears (5), and sometimes a first inversion chord (6#).
Kirkpatrick's explanation
Here is and excerpt of what Kirkpatrick has to say about the harmonic structure (see also the image below).
The fundamental bass is never state entirely in its most elemental form, as quoted here (Ex. 1), not even in the Aria....
Certain alterations to the fundamental bass are to be found. For example, chords of the sixth are interchanged with their root positions, and vice versa. It even happens that a six-four is substituted for a sixth-chord. The bass, the third, the sixth, or even the fifth is occasionally sharpened or flattened. In some places there is a certain interchange or ambiguous hesitation between the fifth and the sixth, with much use of the third alone against the bass, in order to leave this ambiguity free of limitation or definition.
Examples
Taking the third measure of Kirkpatrick's outline as an example, instances of each option can be found as follows.
3: Variation 1, m. 3
Variation 1 contains only the bass note (E) and the third above (G), leaving open whether it's a root position E minor chord or a first inversion C# diminished chord. Note that the C# occurring during beat 3 is not part of the bass-E chord. Rather, it's part of an A major chord leading to the D minor chord in the next measure.
5: Variation 3, m. 2
In variation 3, the first two beats of measure 2 comprises a root position E minor chord. The C# here is a passing tone and does not affect the harmony.
6#: The Aria, m. 3
Here is shown measure 3 of the Aria. It contains the chord E-G-C#, which is a first inversion C# diminished triad, the C# being a raised sixth above the bass E.