So when I've been changing gears, I noticed that I was rev-bombing every time I clutched in to change.  I struggled for a few weeks on this bike as it is new to me, and thought "Well maybe I just suck at changing gears now".

Nope.  Others rode my bike, problem confirmed.

I think what is happening is a very slow throttle drop.  Where on my old bikes, a flick of the wrist was sufficient, on this bike I have to actually drop the throttle off, wait a second or so, then clutch in to  shift, and it is seamless.  If I quick shift like I do on my other bikes, I get a throttle bomb and a stressed gear change.  Not quite grinding, but definitely not a comfortable connection.

Carburetor was recently rebuilt and jetted properly.  It was timed with a machine so I believe the work is solid.  Before I go back in and do it again, can anything think of what would be causing this?  If I switch gears at about 5k RPM, it's perfect, if I clutchless shift, it's perfect.  But anything over 5k with the clutch-in and I get a rev bomb and sloppy shift. 

Does it hang on high idle when you free rev it?

...improperly adjusted idle screw?

...vacuum leak?

It could be the clutch cable adjustments they had to do to put the carbs back on the bike.  When I was having starting issues last year (tight valves) I also checked the carbs.  There was not really any build up, so I cleaned them and put them back on, but I adjusted the cables way tighter than they were before.  I was mostly going by the Haynes manual, but I think it shifted and ended up too tight once I got them fully in place.

Once I adjusted the clearances and buttoned everything back up I could immediately tell that shifting required me to back off much more than before, and when I'm slowing down to 3.5-4k RPM I am almost not giving it any throttle at all.  I've been riding with it like this for a year, so now it's second nature, but I'm sure it is not how it was before my adjustments.

There are some fine adjustment screws available on the throttle itself, but it will be a decent amount of work to get down to the rough adjustment screws on the carbs.  I loosened up what I could and it helped some, so you might try that yourself.