Yes, there's at least three potential causes of clunking right there.
1) damper rod disconnected will just shove it up and down because its effectively floating in the fork chamber, this until it clouts something to stop it.
2) lack of oil will not control the spring and load input such that it can just hit top or bottom of travel to knock.
3)you're right Ted, in that if you put too much preload onto a spring, then it risks going coil bound (coils hitting each other when compressed) before the suspension is through it's travel. This is viscous when it happens, and generally starts to break components.
Preload is only used as a trim in suspension. If there's alot of preload used then that suggests the wrong spring rate for the application, or someone's trying to use it outside its designed range.
Original spring is specified for median usage to support bike and reasonable range of rider weight. Significantly outside that (sidecar, very big rider, constant two passenger + luggage etc) would need that consideration rather than more preload.
I'd build it with everything correctly installed as original and go from there, adding small preload if needed then. Realistically, about 20mm additional preload on std springs is a practical maximum to work with. Any more points to the need for upping spring lb rate to get what's needed, but at the same length.
It shoukd work reasonably well just all standard Ted, or least of all give you a competent qualified baseline.
