I have a well maintained 1990 3.0 V6 in my Toyoterhome. When the engine is warm both inside and out I can hear a chattering rattle I can trace to the air filter. Is it possible that over the years that some spongy spacer has worn out and I have a potential air leak? Any ideas?

 

Replace air filter. Then you will know.
Can you shoot a video? Youtube it and link it here?

Rattling is can be anything from a loose plate that reaches its resonant frquency at points in the rpm band to a timing chain or bearings.
Gonna guess connecting rods

 

It has a new air filter which doesn't fit tightly for reasons I'm trying to learn.

 

What air filter did you buy?

I prefer the Genuine Toyota air filters.

They fit just right every time.

 

What spacer? The only soft material other than the paper filter is the foam/rubber gasket that surrounds it. That gets replaced with every filter change.

This ^^^ saves you labor and time to just use OEM.