What steps should I follow to insure my Rapidweaver install survives a clean install of El Capitan? Worried about plug-ins and stacks…
I wouldn’t have thought anything about the 10.11 OS install should touch 3rd Party Applications or their dependent files.
You should certainly ensure you have at least one backup of everything; but you do that anyway, don’t you 
?
Officially, we don’t suggest you install El Capitan until Rapidweaver (and all of your other software you use) has stated full compatibility. Until El Cap becomes a GM, nobody knows the full extent of Apple’s changes forthcoming. We plan to be fully compliant by the time of its official release.
Until then, it’s officially unsupported.