I'm with ya in leaning towards the clutch, and here's why (minus any useful technical language
).
When shifting WITHOUT using the clutch, going up the gears (1,2,3,4) is easier than going down. It seems to get a little harder the lower you go and the transition between 2nd and 1st gear can require quite a stomp on the lever if rpm's are already high to begin with. I attribute this upshift/downshift difference to the engine being happy to drop some rpm's while going up the gears and unhappy to be shocked into high rpm's while downshifting.
I'm leaning away from the transmission 'cause I would think that a problem in the tranny would show up in a specific gear and not over all gears. Three shifting forks, lots of meshing gears, etc.... Not one unifying component that would cause the same problem through all gears, as far as I know.
The shifter mechanism is a real puzzle to me and I've only really looked at it this year. Still, I would think that problems here would result in things like not shifting at all, frozen lever, shifting in between gears,etc...
I've had to re-adjust the clutch on a couple engines after the first 100 miles or so. Once everything's settled, I guess. Also, the heavy duty springs seem to need a lot less slack at the lever than the stock ones. My buddy liked about 1/2" free lever play(sloppy loose) on his stock 750 clutch. I've had to take all the slack out of the lever, and even more on occasion, in order to get the clutch to fully disengage when using heavy springs w/ new clutch pack.
By the way, congrats on getting the bike up and running so quick. I'm impressed