I've just tried to set-up the TDM's suspension starting with the front end (that's probably wrong for a start !). Using the old cable tie on the fork tube method and aiming for 30mm static sag the best I could get was 45mm - I haven't ridden the bike yet but I wonder if I need stiffer springs ? Surprised though as I'm only 72Kg.
The setup guide is great if you have a modern race machine with suspension directed towards maximum control and doesn't really take account of the oddball arrangement you are faced with owning a TDM.
You'll never get the suspension to work within the parameters the guide suggests. sag figures etc.
But you can still setup the TDM to work well.
Your aim is to get both front and rear suspension working together in concert. Use an appropriate amount of preload on the rear, don't over damp the action and find front end settings that complement what you have at the rear.
Just investigate how many times Yamaha have updated the front end springs throughout the 900's evolution.
I'm on the heavy side, so must weigh in at 120kg with gear. My Mk2 is sweet fuelled up and loaded with panniers and camping gear.
But just try backing settings off when I'm not loaded. The ride changes as the fuel tank empties, upsetting the balance.
It's just a waste of effort, so my solution is just to leave well alone and ride the hard/balanced settings, as they're on what you could call the soft side of hard anyway and move about to compensate..
Simply put, it's a compromise and don't waste your time trying to achieve the impossible.