To pull a wheel with the stock forks with dual disc will require you to pull the caliper off one side, no clearance for it to slide past. I don't think you have to pull the caliper arm but you might. Anyway, it is more steps and a little more involved to do it when you have dual calipers on stock forks.
There are several threads on other forks being fitted for modern two pot or four pot (piston) calipers. GSXR and R6 are the most popular and I think someone even did a CBR600 fork swap.
With those changes they often went to a 18 inch front wheel as well. The GSXR and R6 standard fork (not upside down -USD fork) can be done retaining the spoked wheels but expect to spend upwards of $800-1000 for just the fork conversion, not to mention the extra for the wheel and new tire.
Most will go with a wider rim in front and back using an aluminum rim from Sun or Excel to fit a little larger rubber. I like the stock sizes.
The R6 forks can be fitted with a top triple tree from a FZ6 that has handlebars, for a riding position where you aren't leaning forward as much.
Rear sets work best with cafe bars/clip on bars so, consider that as a possible road that changes the riding position as well.
COgnimoto sells a hub that can be used on the GSXR or R6 fork conversion.
You only need a modern big floating rotor (295mm and up) on one side for great braking, no need for dual discs with a modern fork and brakes.
The R6 conversion uses a CBR600 F2 rotor with the Yamaha R6 or FZ6 rotors that are two piston or four piston calipers, FunJimmy did a nice write up of his conversion with this setup. He did a lot of hub machining using the stock hub...300-450 to get it done usually...
If you have access to lathe and a machinist friend then your cost could be less.
Depends on how much you want to spend. Initial toe into the pond of upgraded brakes is easiest with the stock twin caliper setup on stock forks. Racetech gold valve emulators, with new good springs, and upsized MC to handle the dual discs. I think you can get FA31 pads in semi sinstered composition now...used to be only the organic pads. That helps improve braking as well.
Oh, the other thing you need to do is to install braided stainless teflon lines (Slingshot Cycle has them inexpensively) for the brakes. Shaun can hook you up with lines for a setup of single or dual caliper.
David