I've been struggling with erratic focus and image sharpness with my 600/4 and the 1.4 and 2x extenders mostly because I'm an old fart and learned photography in the pre-computer age when photographers were made of iron and so were cameras (figuratively speaking).

An F1 coupled with an FD600/4.5 didn't care how you put the extenders on, so why should these new gimcrack computer thingies care? They're supposed to be smarter than ol' dumb-ass hardware, right?

Actually, no. They are only smarter in a stupider way, in that the complexity of doing one job well makes them vulnerable to how you do your job and attaching teleconverters is a prime example.

In order to avoid confusing the now very sophisticated software, you MUST put the teleconverter on the lens before you attach the camera so that it's tiny brain records the system as a whole. And it doesn't matter if the camera is on or off, you still have to feed it the pablum with the right spoon - lens/converter THEN camera. Likewise  in reverse, perhaps, when removing the converter, although I haven't tested that, yet.

I'm not sure where the little darlings are going wrong, perhaps it is in confusing the microfocus adjustment, but I rather doubt that since when it gets screwed-up, it is plain that there is no plane of truly sharp focus in the images, everything is soft and microfocus should not throw the lens that far out of whack.

If it were up to me, since the telextenders are only intended for the big prime lenses, the manuals for those lenses would all have a warning on the top of the first page in big letters as well as everywhere in the text that refers to the extenders, focus, microfocus adjustment, AF and anything else remotely relevant, not just a routine reference on page 139 or somewhere, as if it wasn't all that critical. And it would include a full explanation of why it is so (I hate authoritarian "Thou shall nots").