I did a search and found a few old threads, but no complete directions on how to remove the side panels on a 2004 MCS. Hoping someone may have some pics or tricks on how to remove and put back on without breaking clips

 

Mostly, be gentle. Some clips will already be broken from factory install, so expect to replace a few anyway.
Pull the rear seats out, remove the screws that hold the panel around the edge near the trunk door, you can get fingers in where the screws came out to start peeling it off, you can similarly get it off if you work near the main door.
It will easily pop off the clips along the window, and there's no clips at the bottom, you just lift once everything else is free.

 

Well said GBMINI.

 

That is my least favorite thing to take out of a MINI. Not too hard though. Just really big. And I would also recommend to unhook the rear seat belts also. If you don't you'll see why you should.

 

+ 1 I did that also when I decided to sound proof everything back there

 

Getting the panels off were a cinch compared to getting the seats out so you could get to the panels, IMO. Agreed on the seatbelts. The whole job is a lot easier with two people because it is an awkward piece to get out of the car (and the rear seatbacks are too).

 

Thanks everyone!