I'm sure a lot of other people on here know more than I do about it, but I've done five or six of this type of swap now. The latest was a Suzuki RMZ450 front end on an '82 XS650.
I always take both sets of triples to my machine shop and have them press (or otherwise fit) the stem from the old bike (in this case xs650) into the lower yoke of the donor bike triple (in this case RMZ).
I always upgrade to needle bearings (whichever set fits the bike, not the donor front end).
As long as the new height of the steering stem (measuring from top of stem to the surface of the lower triple) is the same as the old height, everything should seat properly.
In most cases, you'll have to "sleeve" the center hole in the upper yoke since the XS650 stem will probably have a smaller diameter than the beefy aluminum sport bike stem.
Only once did it fit without a sleeve ('04 Gixxer1000 on '78 KZ650). Fit perfectly without a sleeve.
If your machine shop has never gotten the stem out of a sport bike triple, pass this on. MOST SPORT BIKE STEMS HAVE A SNAP RING THAT HOLDS IT PERMANENTLY IN PLACE IN THE LOWER YOKE. This means the stem can't be pressed out. The way to remove it is to drill it out (from the bottom, of course) until the base of the stem is paper thin. At this point it can be removed. There might be another way, but this way works for me.
Same with all this stuff. I'm sure there are better ways. Each time I learn how to improve the process.
http://www.johnryland.posterous.com
Lots of the bikes on my blog have front end swaps. Check it out.
HEY OLD DUDE! What's your plan for that spoke wheel on the Gixxer F/E? I was going to do that but got frustrated trying to figure it out. So I went with a modified (shortened) supermoto setup. Love to see it when it's done!
JR