While replacing my throttle linkage boot today, I decided to remove the entire linkage and clean it up a bit. After wire-wheeling the pieces, I noticed a little rubber plug among the parts but don't know where it came from. Where does this go?

Looks like the rubber plug for the AFM's idle air bypass adjustment screw hole.  On the lower right corner of the side of the AFM, by the black cover.  Tends to pop out and fly away when removing.

Isn't there a stopper on the clutch peddle or one of the peddles?  

Was it in the cabin?

21 minutes ago, siteunseen said:

Isn't there a stopper on the clutch peddle or one of the peddles?  

Was it in the cabin?

That's a good one.  

Show the back of the piece.  Is there a hole that fits over a nut or stud?  The AFM plug is solid.

the back has an indention, and is tapered on the front.

Maybe a PO lost the original rubber cap for this linkage, and used the one in your hand? Although it seems small, and might not be hollow on one side..

1 hour ago, Reptoid Overlords said:

the back has an indention, and is tapered on the front.

I meant that the OP should show the back of his.  I've never seen one of yours on an AFM.  I think it might be a hardware store replacement.  I think that the rubber corks are stock, although many AFM's are sealed with clear hard sealant.  Who knows.

Great advice and pictures!

I am missing the AFM plug, but this one is a little too small to fit securely in that void. Both sides are smooth/flat. It had to come from the throttle assembly or something directly attached to it because that's all I was tinkering with yesterday. Both clutch and brake pedal have their larger, clear rubber stoppers and I can't imagine it came from inside the cabin unless it hitched a ride on my sleeve when I popped the pedal linkage off.

Maybe whatever it's from is OK without it. There doesn't seem to be any wear marks on it, so its had a pretty easy life until now.