I know it's a complex thing, trying to find an ideal (or at least acceptable) setup, which is why I did not post a question about how to fix a wobble in a fast corner

As you mention, there are many factors which will affect how the bike handles. I've several different things lined up for this winter, including some machining work on the iso mounts to ensure the ends are actually true. I do not intend to do the whole hog of stripping the bike and sending the frame off to be trued (well, at least not at the present moment), but there's quite a number of things that can be done to remove possible problems. Reading through the website of Parallel Engineering (
http://www.parallelengineering.co.uk/) is informative.
Here's some details of my current setup. It's an 850 MkIIa, standard frame and fork clamps, with Landsdowne dampers in the front forks, Hagon shocks on the rear. A Dave Taylor type headsteady from RGM with the Mk3 spring arrangement and vernier type engine isos. Tyres are Roadriders, AM23 in road compound, pressures were 29/32 psi front/rear. i'm using clipons and rearsets of course, together with a PR tank and seat but no fairing. I do think the PR tank is a bit long though, placing too much weight rearwards. I've always tried for a relaxed grip on the bars, following some interesting experiences on my first real bike, a Honda 550 four.
I've experimented with diferent iso settings, riding styles and body placement, and found that (as expected) tight iso clearances, keeping power on through the curves and placing as much weight as I can on the front tyre definitely reduced the problem, allowing me to give it considerably more stick through the curves. I still did not feel happy about running through Blanchimont flat out though - this to me will be the acid test.
I think the comments about a good starting point for the sag measurements which I recieved from the four independent sources are vaild though. A Commando is still a 2 wheeled vehicle with suspenson, just with a few more variables after all. I would be very interested in hearing what sort of settings you aim for though on your bike.