Hi! If you have changed the exhaust and air filter, you will more or less have to rejet your carb. I did a minor change which included a 5mm hole in the airbox to "improve" the airflow (I know one small hole wont do much of a change, but I wanted to do this upgrade slowly, and do test runs to see what effect the small "mods" would have), but that was enough to actually feel that something wasn't right (didn't give "instant" response to full throttle, and could not feel any gain in HP). I can't tell you how you should rejet your bike, but I would start by increasing the main jets by one size at a time(if the headers are having the same length, you could probably have 2 main jets with the same size), and see if that makes any difference (might have to do some minor adjustments to the jet needles and the pilor screw). The best thing would ofcourse include leaving the jetting to the people at the dyno where they can actually measure the AFR (Air Fuel Ratio).
EDIT: I forgot to add that I have a new KLE with the small jets as stock ('99, so too old for the catalytic converters, but that's not relevant (92 and 95 main jets, instead of having two 112 main jets, as the older ones)). Small washers to adjust the needle might be needed too, but I would however start with the main jets and work my way from there
EDIT*2: The mods I've done to my bike is changing the exhaust, though I did the cheap way and bought an used ER-5 exhaust (~80 dollars), as they have same header length, but just doing that made the bike going lean (no other modifications added), so I installed two 95 main jets, but that were not good enough, so I went with two 100 main jets and that worked like a charm (did need to add a small hole to the airbox, as it went a little bit too rich (but not by much)). Later, I decided to get myself a DNA filter, and it felt like it barely gained anything, so I ended up with getting two 110 main jets (could not get 105), and shimmed the needles with a small washer on each needle, and added an other hole to balance it (5mm each hole). I can't tell for sure if the bike now could be a little rich, but I'll take a look at my spark plugs later to see, but I can tell you one thing - it did help a lot with the performance (no dyno, though the change were noticable (and by much, I would say)). I took a small look on the spark plugs on normal riding (never did any "real" checks, which includes doing WOT on a straight road and check the main jet from there, which I probably should have done), and think that they looked good (but that doesn't tell much about the main jet, but I do not feel any hesitation nor stumbling on full throttle, so I hope it should be fine)
I can not guarantee that my settings are correct, but as I do not feel any kind of hesitation, and the spark plugs did look fine, according to me (if, by anything, could be a little bit too rich, but I'll take a look later with some extra miles on it and decide from there)