What I'd really like to do is leave the double scanning in place & figure out what tests my 2.6 machines are triggering & compare those to the ones 3.0 triggers. Is there anyway I can do this without touching the conf on my production 2.6 machines? I'd like to set it up where I insert the headers above for 3.0, but leave the X-Spam-Status and X-Spam-Report from the 2.6 scanning in place. clear_headers blew out the already existing 2.6 headers.
Erm.. clear_headers should not do that. clear_headers should only clear your header creation settings, and change nothing at all about the message itself.
Are you sure that clear_headers stomped your ones made by the 2.6 machine? If so, it's a very serious bug in SA 3.0.