It's a shame that the bike itself looks to be in very good condition to be a "donor". Lots of sought after parts on that bike that you won't be using too.
Swapping to a GSXR front end is fairly easy to do these days. Cognitomoto sells a conversion hub to lace to CB rim, but uses stock GSXR rotors, calipers, axle, and forks. They even offer some custom triples and top clamps too.
If you are pursuing a "tracker" style, I'd suggest bars not clip ons.
You'll discover the stock 550 seat hoop has curvature to it from the tank to the shock mounts. It's pretty difficult to disguise it with aftermarket seat cowls. You may be better off having it cut, re-welded with a custom hoop, and flattened out. But this needs to be done someone competent with a welder and using quality tubing.
Carefully disassemble your bike, and save everything. You'd be surprised as to the usablilty of the spares since not all of these parts are made any longer.