So here's the update.  I got her going and did some test riding this morning.

Installed #40 Pilot and #145 Main jets.  Air box cover removed.  Jardine exhaust.

I started at 2 turns out on the air/fuel mix screw as good middle ground to start from.  The bike started up fairly well on the first try after about 2 seconds of starter motor cranking.  I got it to idle at 1,100 rpm and took her out for a short ride.  After warming up, she almost wanted to stall sitting at red lights.  Went back home.  Dialed back the idle and found close to 800rpm. Adjusted the air/fuel mix screw to 3 turns out and that brought the rpms up to about 1050.  That was the best sweet spot I could dial-in and then I reset the idle at 1,100rpm.

I think I had an epiphany moment.  The air/fuel adjustment screw on the PWK40 is located upstream of the slide.  It meters AIR!  Turning it counter-clockwise leans the mixture.  Up until my epiphany, I thought I was enriching the mixture by turning it counter-clockwise (like the stock carb that has the mix screw on the engine side of the slide).  Can you please confirm this? I read it on the internet specific to a PWK carb (so it must be true - LOL).  I do recall this on some 2-stoke dirt bikes I've monkeyed with in the past.

Testing...  My first impression was that the exhaust tone was noticeably cleaner and crisper pitch (not as low and rich sounding).  Starting improved - it's almost instant and maybe 1 second.

Idle is smoother and steadier.  Riding pokey at 15mph in 1st is much more drivable and stable.  Same in 2nd at like 25mph.  Same for 3rd at 30-35ish.  Much easier to hold a steady speed at low/moderate rpm.

Midrange is good.  Acceleration is good.  Response is crisp.

I do have noticeably more exhaust crackle on deceleration especially when chopping the throttle from 3,500+ rpms.  Not terrible.  No kabooms, but you could probably make it happen with a hard chop at 5,000+ rpm.  I didn't try that.  Maybe next time.  My poof (dog fart) at shutdown is a little more pronounced, but not bad.  I kinda like it's little dog fart...

My only minor issue is a rich tendency if I twist for WOT hard and quick.  Power goes dull, sluggish, and flat but it doesn't quite stumble (it might do that next time).  Ease off the throttle a bit and she screams like a bat out of hell!  YeeHaw, hang on!!   It's a bit unnerving.  This condition really only happened in 5th when doing about 50mph and rolling on the throttle hard and quick.  Finessing up to WOT, it doesn't happen.  This is arguable operator error - dumping too much gas in there at too low rpm.
No vehicle likes that (that's why automatic transmission cars have auto-kick down when you hammer the pedal to the metal.  And I really didn't experience it in lower gears when I was getting on it pretty good.  I think I'm okay with it.  I'll just downshift to 4th if I want to go YeeHaw from 50mph.  It's like 100 degrees with 99% humidity in Houston these days.  So the bike is breathing as much water and dragon breath as air!  I suspect this condition will improve and diminish when we get some cooler/dryer air.  I'm not inclined to reduce the main jet size at this time.

Overall I'm very pleased.  The Mikuni manifold with tight clamp has solved my air leak and jumbo jet problem.  I need some more miles to check my MPG.  I did some idling, tuning, and some random riding testing so I won't know until I get some more normal miles on it.  I'm anxious to see if I am at 50mpg or better.