I have finally found a bike that fits me, makes me feel planted rather than perched and doesn’t give me knee or back pain, however, it is an old and dented 29er hard tail running 100mm forks.
How do I transfer this magic geometry/set up to my other, generally slacker, smaller wheeled and bouncier bikes?
Are reach and stack the key measurements or will I be fighting a losing battle if the angles are all wrong?

I would say there’s two parts to this; the contact point measurements (bar height and position, distance to saddle, seat tube angle, position relative to BB etc) which would be relevant for your knee and back pain issue.
The second part would be the overall geometry which may well be more difficult to copy onto other bikes, especially if you are comparing ht to fs, the static vs weighted / active geo can be quite different.
Having said that, it’s easy enough to measure up the bike you like and try out changes on your other bikes to test and see if you like it.