1964 cj5 clearance?

Did a search, with no avail.
Can someone tell me how much clearance should there be between the top
of the transmission and the body floor?
I'm getting lots of "clunking" noise from underneath. Have changed fluid
and found no particles, u-joints tight and greased. Transmission shifts
crisp and transfer case also.
Took the boot off the trans. shift lever and noticed very little clearance
between the trans. and the floor. Like maybe 1/8th inch.
There is no shims between the trans/transfer case support and the frame.
Could that possible be the culprit.
Thanks,
tom:?

 

I would think there'd be mor clearance to allow for body twist, chassis flex, etc. I'd be looking at the body bushings and mounts for collapsing and rust.

 

i think there's 2x shims between thetranny crossmember and frame.prob about 1/2 inch