Lovely bike. I particularly like the retro paint scheme.
I have a couple other things to check on the clutch. Both seem really unlikely on your bike, because you've obviously paid a lot of attention to detail in building it. Stll, I've had experience with both of them happening and screwing up clutch operation on my own bikes.
First, have you checked to see that the circlip behind the clutch basket is still firmly in its groove?
Second, did you replace the handlebar clutch lever? If so, does it have the same distance from cable barrel to pivot bolt as the original? These Doherty style levers were available in different leverages, and the wrong one can make the clutch pull really stiff.
Other than that, as already pointed out, stack height sounds like the only other likely culprit. The clutch pull on a Commando is always going to be stiffer than most modern bikes, even with a hydraulic clutch, but it should'nt be so bad to make riding unpleasant.