I just fitted new donuts and adjusta rides and found it helpful to hold the new donut in place with the spring compressor while i fitted the cones and upper arm, that way i knew everything was centered.
My adjusta rides were on the lowest setting and it was tight getting them to fit with the new knuckles but after a ride around for a few miles i had to adjust them as they had dropped.

Which Moulton cones do you have? The Smooth-a-Ride ones are taller than stock and would leave less slack than a stock height cone.

 With the mini on jack stands. Lay under the tower and shine a flash light into the bottom of the tower. Make sure the rubber cone or spring is centered in the tower. You might not see the tiny metal lip that these components should be inside of. With the suspension adjusted loose but not to loose(sloppy) you should be able to move it, to see if it is indeed in the ring.

New cones will take a few day to settle. I wouldn't change anything till Saturday or Sunday other than to bounce on it some and roll it froward a back a bit as it settles.

89 Mini 998/AUTO (Japan IMPORT)
Ordered and installed complete front set-up (new conest, upper arm rebuild, ploy bushings, adjustable tie-rod, ball joints and sub frame mounts)
Question/Confirmation - Installed new cone, CAr alraedy had adjustable HiLo and installed new knuckle. Adjusted hiLo completely (short as possible) What concerns me is the Moulton HiLo Cones seems to press hard against the bottom stop while still on jacks.
Is that normal, doesn't seem right. Looks like it won't come off the bottom stop even after I lower it to the deck.

Does new cones normally raise the car so high? What am I missing ?