There are oodlums of parallel fifths in the organ passacaglia, but I don't remember specifically where.
Now for the chorales: I was told in theory class that a dominant seventh with all four notes cannot resolve to a tonic with all three notes in four-part harmony. If the augmented fourth is to resolve correctly to a sixth, we will have to sacrifice either one note in the dominant seventh or one note in the tonic.
The implication, apparently, is that a contrapuntally thinking listener will hear that the sixth is not in the same two voices as the augmented fourth.
But Bach resolves full dominant sevenths to full tonic chords all the time! If the greatest contrapuntalist in history can't tell the difference, how many other people can?
Walter Piston does not forbid such a resolution, but says that one way is better contrapuntally and the other way is better harmonically. (That's pp. 155-156 in the 1969 edition.)
In chorale #163, ms 6 in the Riemenschneider collection, there is a diminished seventh with a monstrosity of an incorrect resolution.
I was told in theory class that the diminished seventh is a "pre-dominant" chord, meaning that it can occur next to the next to the last in a cadence, but not next to the last.
If this is so, then Bach breaks this rule at the end of #3.
Tchaikovsky does the same thing in #3, "The Hobby-horse" in his Album for the Young, op. 39.
Besides, he resolves the diminished seventh incorrectly.
I have found parallel fifths in chorale #244, ms. 8; #285, ms. 9; #288, ms. 1; #297, ms. 3.
Do parallel fourths count? Then how about #79, ms. 11; #106, ms. 4; 118, ms. 1;
#183, pickup and ms. 1?
I once played second violin in the b minor suite for flute and strings. The the fugue, there were two places where I played parallel unisons with the viola.
I asked the conductor about that.
He said, "Bach bent the rules, that's all."
Then he added, "They all bent the rules except for Palestrina---bor-ing!"
Once you're written your magnum opus, send me a copy.