I have seen BWV 1006a with 3=f#, but never 998. I shall keep my eyes out for it. I do have an old book with the piece in Eb with 6=Eb.
Addendum : I have never liked 3=f# with the key of D major. You might get some better fingerings, but the tonic chord in the second position is an example of where 3=f# doesn't work well. If you think of strings 4-1, F# A D F# respectively, with 3=f# that A on the 3rd string is now played at the 3rd fret. If you play it with 1 then you don't have 1 to play the F# on the 1st string 2nd fret anymore. That particular configuration happens a lot in the key of D.