But.. while you can happily time the ignition on the wrong stroke, because of the wasted spark, but you can't do the tappets on the wrong stroke, believe me I've tried.
It doesn't matter when you're building it, because the engine doesn't 'know' which stroke is which until you time the cam. Once you have timed the cam you want to be doing the tappets on the cylinder where the pointy bit is on the opposite side to the cam follower, ie you are on the base of the cam.
I got confused about the 1 - 4 sequence at first, (despite it being written on the plug leads), think of it as when you are sat on the bike, its the same way round as you would write 1-2-3-4 on a piece of paper if you put it on the tank in front of you.