Seems my trouble-shooting has migrated to this new thread, so I'll update here...
OK, last night I tinkered and started going back over things....
Main Air Correctors measured out to the appropriate .042" and are all in place.
Air Jet (Jet on left side of carb inlet) were re-verified to be 180s, which I believe is stock.
Did the WD-40 test around the new intake boots... no leaks found.
Removed fuel-line and did a petcock fuel flow test. Fuel seems to be flowing well, with what appears to be normal volume.
Per the DJ tech, removed the air-pods... on the stand, if you go from warmed up idle to WOT, it will stumble at around 2,000, carb slides will flutter up a bit, and then it seems to get past it and revs up.
If I put some wide masking tape across 1/3 or so of the carb inlets, there is no stumble or flutter and it just revs up.
Put airpods back on with approximately 1/2 of the filter taped up and rode it down the road. Was wet outside, so I could really get on it, but it still appeared to have the stumble around 5500 or so.
Removed the plugs and they look like this:
Cleaned up the plugs. They cleaned right up with minimal work. Underneath the little bit of idle residue on them, they look lean to me. If it was too rich, I'd expect to see way more color.
NEXT steps are to verify the actual fuel level in the floats. Hopefully I'll have some clear fuel line today to make that happen.
If all that checks out, I'm not sure which direction to go.
Other things to check are going to be the valve lash, and the Ignition timing. Found the valve lash tutorial. Done lots of those on Japanese and British cars, so it doesn't look like a problem to do. From looking at the screw heads, it appears the Cam covers have been off this bike before, so we'll have to see what we find when I get in there.
Is there an ignition timing tutorial around here somewhere? I couldn't find it on BassCliff's site. (however, it's 4:00am right now, so it's possible I just missed it...

)
Not giving up yet, though I did drag out the stock airbox, just in case... It's kind of a mess and I REALLY don't want to have to use it.
I'll get this figured out eventually.