Setup Finite Elemente Master Ref Rack

What do you mean by "worse", can you describe the difference?

I have built and bought various stands over the last twenty years, and everytime I changed the stand, the sound quality was affected, sometimes better, sometimes worse.

Responding to your questions within the limits of my experience with using a Master Reference rack for a few months:

1. Anything to pay attention to when putting the shelf spike on the cone? Just check that spikes are adjusted that so that shelf doesn't wobble and shelf does not touch rack.

2. Should the foam be removed? No, they help center the spikes in the cones.

3. Does it need to run-in? I don't think so - not sure what aspect of a rack will need running-in. However moving your components between racks implies that your components may need to run-in again (some pre-amps, amplifiers and DACs need a few hours to a few days of use or been left on for optimal sound quality). Also some cables don't respond well to been moved and bent, and may take a few days to settle in.

Is it the other factors (such as electricity) affecting the sound?

It worthwhile checking if anything changed when you re-assembled the components into the new rack such as type of mains cable, order of plugs in the distribution unit/conditioner, and dressing of the cables i.e. ensuring the mains cables are not close or in parallel to your interconnects.

One aspect to consider is the physical size and positioning of the stand - in particularly imaging is affected by the height of stand if positioned between the loudspeakers.

And finally, consider trying the rack without the Cerabases and use the spikes as per your Signature rack.