Say you have two rebuilt transmissions.... a TH350 and Muncie. How long could they be stored before things start going funny? Should they have a bit of fluid in them?

 

I would keep as much fluid in them as possible...and for length, I put a TH400 in my car that had been sitting in the garage for 12 years. It was rebuilt, taken out of a car 1 year later and then sat for 12 years. I just pulled the pan, changed the filter, changed the input / output shaft seals, the gear selector seal, and the dipstick grommet.

Now it sits behind a 492HP 455 and it's holding up fine. I'd say you're ok to let one sit as long as it's inside.