lol yeah the YZF axle traps a few people... there's no science to it, all you need to do is jack the front end clear of the ground, leave the pinch bolts on the "allen-key" side of the axle loose, push the axle through the wheel etc, and tighten the axle nut all the way up. Take the bike off the stand, bounce the front end up and down, and check to see if the forks are compressing and rebounding freely. (shows whether or not the forks are aligned properly, or whether they have been "pulled in" at the bottom.. )
The stepped shoulder on the axle should be hard up against the axle spacer, and the stepped shoulder will be well clear of the fork leg... ie, it wont be flush with the fork leg. With the fork legs aligned vertically on my Blitz, and the spacers in the correct spot etc etc, the allen key end of the axle sits about 4mm INSIDE the outer edge of the fork leg... if i ever stop working and get to go home, i'll try and get a pic up of it..
i wouldnt be too worried about snapping the YZF axles with the way they mount... i've flat landed a few 80 footers and a couple of 100ft dirt jumps on both the 400 and the 450, and both are still straight as a die...
bit odd that the brake rotor and caliper didnt line up... if memory serves when i dummied all mine up, the caliper lined up fine, as they run the same axle, rotor and caliper offset as the YZF's... I dont think you can use the Blitz caliper and wheel on the YZF forks, as the Blitz disc rotor is of far bigger diameter than the YZF rotor... need the black caliper mount to enable the caliper to "reach" around the Blitz rotor..