Well I know this thread has been "complete" for quite some time, but just a final update on tuning...
I finally got around to getting her running better this week and man I really should've done that like a year ago... the difference is amazing!
Turns out I wasn't rich at all. What I thought was bogging off idle was hesitating. What I thought was surging at low throttle openings was a flat spot and stumbling. The pops on decel weren't excess fuel igniting.
I learnt all this by getting some needle shims off eBay and initially taking the needle back to stock and shimming it up half a notch (I had it one notch up after the rebuild). The bike was almost unrideable at low throttle openings. Hesitation off idle, stumbling until about half throttle... horrid! Went up to three quarters of a notch, better but essentially still the same.
At that point I figured I was waaaaaaaaaaaaay too lean so I took it to one notch up with the E clip and shimmed it another half notch. That was more like it! Still a little hesitant, almost a stumble but not quite, and much reduced pops on decel.
Final needle setting is maximum richness of two notches richer than stock and it's now completely transformed. No hesitation, no stumbling, and I didn't notice any pops on decel after she was warmed up. I'm stoked!
Here's the test ride video from today:
http://youtu.be/z0kZX5McUzM