Here's what I do when I have an issue similar to yours.
First, once you determine that something isn't about to fall off, just drive it.
The problem will likely get worse over time. Once this happens, it should be easier to diagnose. Whatever is making the clunk will become more loose, and show itself.
Carl


1952 5-window - return to "as built" condition | 1950 3100 with a 235 and a T-5 transmission