Hello David,
I had the same problems with my 2012 model TDM 900, this is what I did after testing a few things.
Lift your fuel tank and remove on each side 10 cm foam it will give you more air,modify the cover of your air box as I did ( see short movie ).
Remove the foam at the air inlet side.
After that relocate your A.I.T sensor too the front of the bike.
Set your Co settings on both cylinders to C1 25, and C2 25 with stock exhaust, with open exhaust Co settings to more then 50 on both.
Be sure your engine runs at idle on 1200 to 1300 R.P.M when its hot.
Whit these simple mods your bike must run very smooth in low R.P.M and stronger and faster.
Every thing is reversible, and it will cost you almost nothing.
I fixed 30 bikes here in holland the same way, and all of them runs very good now.
With half open exhaust you can do more with the bike.
Greetings, Frits from Hollans