Tom is correct on the sizes of the big bores....I regret every going past the 685 cc size! It was the best kit by far! It lasted 5 years without a seconds trouble. The only reason I started the stupid climb up the cc size was to fix dirt scoring my 685 kit. I'm now at 705 and am seriously thinking of selling it and going back down.
I have Megacycle cams, the .410 lift selection. IMHO, unless you have a better carb which I do now, a flatslide pumper they are not worth the money either!
But if you do have the 685, stage II headwork done, cams and the flatslide carb....oh and any slip on exhuast using the 08 header or aftermarket header....you will own a very strong KLR that will scream past redline at a whim! I run 16/42 gearing and can easily lift the front wheel with slow roll-on throttle any time in first, not quite as easy in second but it still goes up and if you can clutch shift or wheelie I'm sure it would go up in third just as easy. I don't....too scared to come off in my brittle old age!
I have let a few close buddies ride it and the smile on their faces is all I need to know they aprove of what 's been done....lol. Plus riding their slightly modded(bigbored 685) bikes trying to keep up with them is useless!
Some will say BS but until you have felt the difference.....you just won't know for sure! It costs much money to get your bike to this level and is it really worth it? Ask me when I stop to wait for you....lol.
OH, and buy that 99! You will need to change the stator in it to make it compatible with your charging system but it's simple. You can either just swap the rotor and stator cover with stator in it as a whole or swap out just the stator and install it into the newer case and also the rotor. That rotor from your older engine is 10% lighter and will spin up much faster than the heavier rotor, yes I have done that also. But I took it back out as I was eating rear tires!!!
There are many ways to get a KLR to move out and I have done almost all of them over the years. All of these so call useless smaller mods which if dyno'd singularly wouldn't show any power gains but when you add a bunch of them together, you will notice them for sure! Again there will be some who will say BS again....but again until they do the work and see for themselves.....they will never know.
Buy that motor and do it up and ride your old one while doing it.