First and foremost should be getting the fork sorted out. That's an immediate safety risk.
If its got to come apart for seals, go ahead and toss in the proper springs for your weight and riding style. Most 600cc bikes went with springs that are much too soft, which helps with ride quality at the expense of handling. Seems like the Japanese engineers, and quality people all weighed at least 40 lbs less than the typical North American, and selected springs that were 'just right' for a rider who weighs around 140 lbs in full riding gear.
This is also an area that just about everyone ignores. I've opened up the forks on bikes I've bought, and found fork oil that was 'factory', but sure as hell wasn't 'factory-fresh'. If you're going to replace the fork seals, do as RJ recommended and change the springs for your weight/riding style, but don't ignore the fact that fork oil is available in different weights which can be mixed to better suit without needing to go whole hog and change the shim stacks, etc as well.
Personally, I reset the suspension to stock settings and:
2. Note what needs to be adjusted in terms of preload, rebound, compression.
If you're within a couple of clicks of reaching maximums, you'll know that springs/oil weights/air gap/shim stacks/valves will need changing. It means your ride is safer, more comfortable and you'll be a hell of a lot faster than any exhaust/jetting/Power Commander mod will ever make you.
I'd recommend swapping out that rear tyre for a matching Diablo II before you go for suspensions setup, as this will have a big effect on what will need changing.