I do not own a Zone VI (well I own one of the tripods). I've watched an friend use his, no problem using a 90 or 75mm with a flat lensboard and bag bellows. the lensboard is quite small on the Zone VI (it is intended for field use), so I don't think a recessed board would be practical.
You can simply measure and see what lenses will work in "MOST" LF situations. A 90mm lens needs very close to 90mm between the lensboard and the groundglass (at infinity). 90mm for us metric phobic Americans is about 3.5 inches. If you can put your lensboard about 3.5 inches from the groundglass, you are probably "good to go".
There were a few variation in the "Zone VI" 4x5 camera. Originally it was a custom Wista, then Zone VI built them (or had Ritter do it for them) and finally they had Wisner make them. My second hand experience is with the middle (in house / Ritter) version.
Is it possible your 90mm lens was bad? Did you ever see it focus on any camera? Just wondering out loud, perhaps someone put it into a shutter with really incorrect spacing.
Hope that helps.