Well, I'm embarassed & relieved. I'll go ahead and explain this since several of you tried to help ol' misguided me. Also, I don't want other folks to find this "problem" & try to "fix" it now that I've brought it up.
When I went to the dealer today, I made a point to check other Yamaha's front forks/axles to see if there was something I'd missed. Turns out the the shop's used '05 FZ6 & the new FZ1 (could have been an R6, I was only concentrating on front wheels) both had similar gaps between the right (from rider's perspective) fork & wheel collar, just like mine. FZ6R's have changed their front axle design, so couldn't make a comparison. So I come home perplexed, take the axle apart a few times, and finally - Eureka! The hole on the right fork has the same diameter all the way through - the axle could go completely through it if the left fork wasn't in the way! To show you what I mean see photo with axle put in backwards through the right fork.
View attachment 13574
Sorry it's a bit dark but if you look closely, you can see the largest part of the axle going all the way through the fork, only stopping because the wheel is in the way. So theoretically, our bikes don't even need the right fork (if you drove on an ultra-smooth road with a super strong axle). The axle is built to hold the wheel together using just the flared end on the right side of the axle and the threads in the left fork. The right fork is basically for stability and balance(and for the FZ6's beautiful symetry

). Soooo... don't worry about the gap if you have it.
Thanks all for the suggestions and help.
"When in doubt, dissasemble and reassemble is my motto." wrightme 43
And special thanks to wrightme43.