I want to make sure you are using my new 3rd edition, almost finished, but downloadable in its entirety. Trills are treated in sections (9) and (34), link at bottom. In Bach, trills are not fast, but you need to be able to play it independently of the other hand, so you have to be careful so that it ends at just the right time. It helps if you start the first two notes fast, like a parallel set.
I'm not sure you got it right.(1) practice intervals: 3.1,3.1, two intervals repeated as quickly as you can, then three, then a quad. Don't go to the next until the first is satisfactory. Then two quads, then three, to a quad of quads.(2) practice PSs: 31, get it to as fast as you can, also 13.(3) now gradually substitute the PSs into above quads: 3.1,3.1,3.1,31. when this is good, substitute two: 3.1,3.1,31,31 etc, until you have a quad of PSs.Satisfactory means a quad a second, but beginners will be slower.THEN you still got the big job of concerting those series of PS quads into trills, once you get up to speed. Staccato practice is a good way to do that.If your PSs and repetition abilities are good, you can bypass all this and go directly to PSs: practice 31, 13, then 313, 131, etc., adding a note each time. But each PS has to be really fast before you can go on to the next (unless you are a beginner). However, Bach's trills are not that fast.Do not count notes in the trill; Bach is trying to teach you to trill in one hand (at any speed you want), independently of the other hand; yet be able to terminate the trill at just the right time to join the other hand at the end. Too many teachers "simplify" this by counting trill notes, slow down play so you can play it, and gradually speed it up. That doesn't teach independent trilling skills and next time you meet something like this, you have to start all over again, whereas if you learn trill skills, next time, you can do it instantly even if the circumstances are a bit different. That's what Bach had in mind.