W140 95 S420 tool kit
 

Is something missing from the tool kit over the spare tire? There's a small cubby to the right and a large flat cubby in the lower right that are empty. Should anything be in these cubbies?

Thanks,
Sixto
95 S420
91 300SE
87 300SDL
83 300SD

I'd venture a few guesses:
The large flat one probably for putting small parts there that you may have taken off, or else a cheap pair of work gloves can lay in there.

On the smaller one it looks like possibly if you had locking wheel bolts that the "key" for removing the locking bolt (Not like a blade key, like a tool that would go into the wheel wrench) would fit in there, looks like the right dimensions.

Gilly

the large hole has shorter bolts - used when you have alloys and use the spare (steel)

the small hole is empty on mine as well...

guy

On my '96 W140 Coupe, the large opening came from the factory containing a plastic package containing 5 lug bolts that match the front alloy wheels...
The front and rear wheels on my Coupe have different offsets... and the front and rear lug bolts are different lengths.
The spare tire/wheel is an alloy that matches the "front" with 51mm offset. According to the owner's manual, if you have to replace a flat front tire, just use the original bolts.
If you have to change a flat rear tire, you're supposed to use the bolts in the tool kit with the spare... and repair/replace the flat tire as soon as possible.
If you have four identical wheels on the car, and the spare is matching ... my guess is that the space is supposed to be empty.
Not sure what the small hole is, but I agree with Gilly about its intended purpose for the wheel key. That's what I use mine for.
Can post a pix is anyone's interested.
Hope this helps. KenP