First, my disclaimer - my bike is a 78, so yours might be different. Firstly, on mine, the clutch rod must be installed from the front of the input shaft. This is in order that the felt seal is compressed and fit into the correct position in the bore. The transmission is then mounted. Then the throw-out bearing parts can go in. Then, for ease, I would loosen and back out the adjustment bolt on the operating lever.  Then remount the lever with the boot. Install the spring.  Connect the cable and adjust the cable length so the arm rests almost parallel with the back of the gearbox (or use the 201-203 mm setting). Then adjust the bolt on the operating lever to achieve the 2-4 mm free play at the hand lever. Lock in place. 

The Clutch parts changed in 81. The adjustment procedure is the same though. Tom Cutter has a good write up on his web site. The push rod needs to seat in the clutch spring plate. This should not be a an issue if you did not disturb the clutch while the transmission was out. You need to be sure that the throw out bearing is not hanging on something. I always loosen the adjustment bolt on the clutch actuating arm before I assemble it.

The Max part fiche mentions the "new" piston that does not use a bushing that is not used on the "old" piston. Sort of implies that you need to use a different rod. I would talk to who rebuilt the transmission or who you bought the parts from.