Well I'll be dipped in shit.
It's only taken a couple of years, but I finally got the bottom of my rich carb situation and rough idle. Went for a ride with a mate the other day up into the hills, and while hoovering down a poutine it occurred to me that maybe the pilot jet that I've been assuming was a size 40 because it has 40 stamped into it wasn't 40 after all. Maybe a PO had reamed it out, made the thing bigger for whatever reason. By this point I'd pretty much tried everything (everything that I could find out anyway) and no dice - this thing ran rich no matter what.
So yesterday I went to see my friend Brian at Moto Expert in Laval (anyone in the Montreal area that needs any help with their dual sport then he's absolutely the guy to go and see) to go pick up a guaranteed OEM Keihin size 40 pilot jet. While I was there he lent me a fully Dynojetted-out CVK40 carb that he's run on his bored-out (to 685, same config as mine) KLR which had run like a champ. That way I could sling a known-to-run-great carb into my KLR and use it as a benchmark.
Got home, cleaned up his carb complete with the DynoJet internals and 40 pilot jet and whaadya know, bike fired right up, idled beautifully (and waaay quieter than before) and rides like a new bike. I'm not even kidding - Like. A. New. Bike. No more stinky exhaust, beautiful idle, unbelievable difference.
I compared the 40 pilot from his carb to the supposed 40 from mine - the hole in mine looked to be about three times the diameter. No shit is was running rich. Less reamed-out, more like jet sabotage. That explains why the plug would carbon foul after a couple of minutes idling, and why I absolutely never needed to pull the choke. Ever.
So, the plan now is to ride the bike, give it some WOT and give it a good stretch. Then I'll pull Brian's carb - mimic the set up with the DynoJet kit that I bought a year or so ago (and pulled because it made the bike run like utter shit - not surprising given the pilot jet had a hole big enough to drive a bus through) and hopefully be done with it.
Moral of this story folks - never assume the jets are what they say they are on a previously owned bike. I know I won't ever again.
So yeah, a bit more experienced today 8)