Mine is the tried and true KLX set-up and is a recipe that seems to work for the vast majority of KLRs. Sometimes the recipe will require a bit of tweaking by doing a half-clip's worth of needle adjustment with a #4 washer.
Begin with a KLX needle with the clip set at the second position down.
My carb, an '09, came with a 145 main jet. I have 1" holes drilled in the airbox and a modified airbox door. I use a GSXR750 pipe, which is fairly open. I dropped the main jet down to a 142.5. That gives me an air/fuel ratio of about 13:1 from idle to near redline, as measured with an 02 meter.
I had some excessive popping on decel and changed the idle jet to a #42 to get rid of that.
I did drill the slide to 7/64" but I'm not convinced that it is worthwhile. The CVK40 depends on the vacuum to raise the slide; the hole that is being drilled is essentially a transfer port that allows air to come out of the upper chamber as the vacuum pulls the slide up. You can see how, if that port is too large, it could defeat the vacuum to a degree and prevent the slide from rising (or, at the very least, the slide would flutter). That's why drilling that hole too large causes bogging.
pointed out, a pinched diaphragm has the same effect because it defeats the vacuum and the slide won't rise completely.
Since it is vacuum that is raising the slide, rather than a direct pull from the cable, there is a lag. This is the throttle response that drilling the hole is supposed to improve. If I were drag racing the KLR or if I were the type that goes WOT off of every green light I might think that quicker throttle response is really important. But I'm a fat, tired, old man and I don't do that shit. Since I don't slam the throttle open I don't notice the throttle lag. I don't think most people do, either, but they get caught up in "doing all I can to get as much power out of it as I can" even though they've no use for it. That's why I question how worthwhile it is.
To recap, a KLX needle with the clip in the second groove, a 142.5 main jet, 42 idle jet, holed air box and a freer-flowing exhaust. Drilled slide, meh.