this will help you out.. sorry I didn't get to you sooner.
Once upon a time I found an abused Sega 2/Mega CD combo at a Goodwill (second hand store)
It had no power supply(s) and seemed to have some sort of liquid in it (motor oil or soda?)
for $2.50 I took it home, disassembled the Genesis portion and cleaned everything (won't get detailed so I can get to the point)
The Sega CD's Pop Top door was missing it's spring and there was some damage to the inside including the spindle and magnetic carrier support (piece on the lid that holds the CD to the spindle).
What I did, (and what you want to do) is find an old portable CD player. take the middle bit that the CD clips to and replace it with the one in the Sega Mega CD console. Also remove the magnetic carrier off the top of the lid (no longer needed). Think of how a Playstation 1 was designed... that is how we are changing this console. The shaft should barley protrude over the CD clip and the CD should spin freely on it. It might be trial and error to find a CD player with the right size spindle clip. A PlayStation 1 (original model) will fit too, but please don't destroy one of those just to get a Sega CD operational. Also, to be clear, the motor and shaft stays, only the CD spindle plate (or whatever you want to call it) gets exchanged and the magnetic support on the lid gets removed.
you shouldn't hear the CD spin up, the reason why you heard mechanical noise when you flipped the unit over was because the plastic magnetic carrier was scraping on the lid. It is only a 2x drive and shouldnt rev like 360's jet engine drive.
I hope that helps some people out there... I'm not 100% sure if it will help your unit though as it might have other goblins to deal with.
try operating the system partially apart, use your finger to trigger the door switch to make the CD spin-up...
there are so many troubleshooting techniques ... but I think we all give something a quick smack to determine if it is broken right?...
These images should help. I had access to the one I modified/fixed and a untouched original.


Oh, and I never mentioned... yes it worked perfectly after the repair!

Thank you