How close preamp and CD player

I have used these exact units together, with the CD on the top shelf and pre just below. It worked perfectly. I don't think you should be concerned about any noise somehow being generated between the units. More important is ensuring there is adequate ventilation around and above the pre. I suggest at least 3" for each side and the top, and an open front and back. If you have less clearance, you should consider a small 12v fan. I run them at 6-9v to reduce the fan speed and thus the noise. Just find a cheap wall wart with the right voltage.

I have CD3MkII(top shelf of SolidSteel 5.4) and LS-25MkI(shelf below). No problems at all.

P.S.
Are you running balanced or SE from CD3 to LS?

I'm running balanced Discovery Essence. Thanks for the responses.

I have about 2 1/2 inches on top, open on all 4 sides.

that should do