Good on you having a job as a motorbike wrench, doesn't matter about the Harley aspect, two wheels good four wheels bad!
Could I ask if you noticed a change in the shift feeling or action before getting stuck in second gear? I ask this 'cause I've noticed my shift action seems to be getting less affirmative (less clunky?) clicking into gear than it used to be and i wonder if the pawl spring is on it's way out.
I found the gearbox shaft and shift fork re-assembly reasonably easy with the Clymer manual for reference, as you know the rear cover has to be heated (hot to touch) and put the shafts in the freezer overnight as an extra help. As far as I recall, I placed the intermediate and output shafts, along with the rear and mid shift forks in together first as an assembly, you'll hear the shafts drop into place in the bearing receptacles.
I have to admit I farmed out the output flange removal which I'm glad of as the previous ham fisted assembler jammed the flange nut by using no washer with the nut. I didn't know this before I farmed it out, the BM trained mechanic wasn't impressed and it took him half a day to get it off, most of it fabricating a removal tool. In my more novice state I was glad I didn't attempt it in my garage...
As George and Tony say, buy all the lip seals (input, output, selector shaft and clutch push rod), I bought a new clutch thrust bearing and clutch arm rubber boot) and lube the input shaft splines with high moly paste. Remove the neutral switch otherwise it'll get knocked and start leaking (don't ask me how I know)
Have fun, all will be good.