Bach and Temperament.
This is a very thorny issue. There are several sources that suggest that Bach liked a full circulating temperament and, indeed, his last organ works suggest that he did. Nevertheless one must take a more nuanced position here.
THE YOUNG BACH certainly was used to mean tone temperament. All his early work seems based on it (sometimes in a very crude manner: long sections on the tonic and then up to the dominant and back to the tonic). He even used f minor for his «Ich ruf zu dir», a very early work (it is to be found in the Neumeister chorales). Now f minor, in mean tone temperament, is quite desperate, which is in keeping with the words (I call for you, Lord Jesus Christ).
THE MATURE BACH. By the Leipzig years he asked for a more tempered - perhaps something like Neumeister - in the organs. Now the organ certainly poses a problem: when tuned, it will stay like that because you actually have to modify the flues in order to retune them. So I think that, at least on the organ, he liked to have a circulating temperament (his disputes with Gottfried Silbermann are well known).
This is important, because the organ, perhaps even more than the harpsichord, sounds best in mean tone temperament (for specialists: because the quints and tierces are tuned pure and therefore strongly beat with the wrong intervals of a circulating temperament).
Regarding the harpsichord, the question is quite different. A harpsichord may be tuned in about 20 minutes, and therefore it may be retuned at will. Nevertheless, I still think that Bach was experimenting with some kind of circulating temperament. He is said to have played the whole of the WTC to his pupils, and nothing was said about retuning. That aid, it is a fact that equal temperament is very ugly on a bright harpsichord. Perhaps he chose the temperament for the individual pieces? This may well have been the case, because his harpsichord works seldom stray too far in modulation terms and use more or less «usual» keys («usual» in terms of a modified mean tone temperament).
Be this as it may, I am convinced that Bach used a rather strongly modified temperament, but perhaps - indeed, almost certainly - not equal tuning. I think it was more strongly modified than Werckmeister's, perhaps the equivalent of a Valotti?
Let us not forget that, with mean tone temperament, even e minor sounds odd ...