They don't necessarily input more load to the frame as, for the sake of this discussion, those forces don't change. There are many things USD forks do better, a few are. The diameter of the fork where they are likely to flex, at the lower triple clamp, is greater so there is less flex of course to make use of that you would need a much beefier lower clamp. Because the lower slider is smaller and lighter there is less unsprung weight (in a nutshell the amount of weight that the suspension has to handle) so the suspension can react to road irregularities better. The part of the fork that slides is lighter so when braking it wont press as hard against the other tube and the suspension will work better while under load.
Its important to remember that at the pace that a lot of people ride, and that the Bonnie can achieve, the better forks aren't going to make as much of a difference than at the pace the Ninja can achieve/will most likely be ridden at.
If you want it you can have it, although you will have to pony up for a chassis shop to make you a set of triple clamps that will take the 54mm or so upper sliders.
The angle I would go with is that if the pre-2005 45mm S3/Daytona forks are long enough you have your triple clamps bored out a little to accept them. Of course then you'll have a cast front wheel and a spoked rear wheel so you'll have to figure out how to either put a spoked back on the front or fit a Sprint wheel on the back.
Mule Motorcycles, who did the Bonnie flat-tracker at the IMS, would probably be happy to help you out with both your Bonnie and your bank balance.
IMS Show Bike
You'd get something sassy like this:
[ This message was edited by: TBSstunta on 2005-03-15 13:31 ]