Hey JTCrow, I'm in the midst of installing and setting up exactly the same thing. Check out my thread below. I went through the various carb mods one-step-at-a-time and at this point I'm at a very similar stage as you, and I'm working on the exact same issue. For the sake of completeness, I'm putting my process comments in that thread (I'm actually logged in to make more notes there, so gimme a few before checking). Here's my setup so far. It's not perfect (I'm overly picky) but it's workable.
No drill on the carb slide
142 main jet (Not the 140 as suggested… Eagle Mike's KLX kit, purchased in Dec.)
Pilot Jet #42 (Eagle Mike, same time)
Clip at 3rd position on the needle, no shim under
Pilot screw at 2 turns out. Note, the original needle has been swapped for an EZ-just mixture screw from CV Performance (allows easy adjustment on pilot air mixture screw, but has a slightly different profile from stock, which seems like it probably matters — see my thread for a visual comparison)
I tuned the mixture screw today, and I think the above is as good as I can get it without changing stuff. This is at 65° weather, 0-300' altitude.
That being said, I wouldn't take this as "advice." I would instead take it as a note, then wait for pdwestman and Tom to chime in. I'm a novice, they're not. Also, I did a lot of reading on old carb threads here the other day. Try searching for "KLX Needle" or "dynojet" — I found that threads mentioning this other manufacturer's needle were enlightening as background knowledge, and the threads themselves often feature discussion of different needles. I also looked at a lot of harley tuning articles that talk about the CV carb which are, again, interesting background info. You can find these by duckduckgo'ing "CV carb needle" and similar terms.
Here's my thread.
I'm curious to see what solutions you come up with!