It may be worth giving Parallel Engineering a call on
07794 637159. They specialise in Commando frames. Based in Shropshire, Google them.
Just looked at their website and they look very competent. If I lived in the UK I'd definitely check them out.
About 6 years ago now I followed the World's straightest Commando article to try and correct issues with my Mk2 850.
My bike had three issues with handling. Firstly at about 80 mph the front end started to feel nervous as if it was about to become unstable. Years ago I had found the beginning of a tank slapper but never pushed it hard to find out. In contrast for several years I had raced a featherbed 500 twin and never ever felt the slightest concern about front end stability.
Secondly if you let the bike drift without your hands on the bars below 20 mph it pulled very heavily to the left such that in order to keep it in a straight line I needed to slide off the seat to the right and hang my body way to the right to keep it straight.
And finally on a roundabout for example the bike felt like it was going around in a series of flops up and down and it was basically pretty much impossible to maintain a nice steady curve.
This was all on a bike with good tyres, properly adjusted isos and as far as I could tell good suspension.
I had the frame checked for alignment on a plane table. It seemed OK.
The swinging arm was badly twisted.
Both rims were well off the centre line of the main central frame tube.
The top iso was replaced with a Dave Taylor unit.
Both front and back isos were replaced with CNW units.
New Ikon rear shocks fitted.
Front forks checked for alignment and parallel and internals serviced.
Tyres were not changed as the were pretty new. Dunlop TT100s
After that the bike became a good handler and no more head shaking.
That Parallel Engineering place looks like they cover all the issues we worked through so I think they would be a good place to try.