Do you really think the OP is considering running without the cap?
When it comes to mechanical issues, it always pays to never underesimate the stupidity of people. Some of the stuff I have seen done would make your hair curl. Nothing can be idiot proofed, the world keeps producing better idiots.
Back to the OP, if it locates in the correct place, the brake rotor is in the correct spot and the clamp holds tightly it should be fine. IIRC the DOHC bikes were a little wider between the forks. 
I'm sure I've done some stupid stuff in my life but there's no way in hell I would ride that thing without the cap. I'm not that stupid! What you said about the DOHC bikes axle being longer than the SOHC axle makes me feel so much better. Yes, everything looks to be sitting right. The calipers fit well, the rotors fits well and the wheel moves freely. I'll try to get some better pictures.
Good to hear you don't belong to the elite world of mechanical dumbarses. I had one come into work a couple of years ago who had replaced the clutch on his ute and now had a shudder. We asked him if he had had the flywheel ground, his response was "Yeah I did it myself."
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Long story short he had ground the flywheel with a 4" grinder.
Anyway, back to the original question, if it really bothers you, you could always have a little machined off the end.
