"Anybody alse have this problem?" Yes I have!
I am totally focusing on getting my BS34s Jetted correctly 81 special. My setup a bit different yours but maybe what i have been going though can help you.
I have mikes XS1 Type Exhaust System and stock air boxes with more air inlets and am at 4500ft.(higher=leaner) I am also running xsJohns custom Needles.
I would say you need to Lower your needles.
After messing with this setup and trying all combinations this is what i did last night its a Huge improvement. I've got 75 miles on it today I am finley making progress, not all the way there yet but closer. , 60-65 was top speed I would up the main then the midrange 35-55 would be to rich.
I have stock jets except, I have the MainJets at 137.5 today with lowered needles it would cruse 70 freeway! but still lean, now my midrange is leaned down with the lower needles I am going to try a bigger Main
Your stock needles are not adjustable (down anyway)
heres some links that helped keep me sane working though this, go slow use your head and ride it alot and read the plugs, think, read more and try the next step.
http://www.iwt.com.au/mikunicarb.htm
http://www.factorypro.com/tech_tuning_procedures/tuning_carbtune,CV,lower_rpm_engines.html
This is excellent direct info about our xs650s and takes a while to digest. need a login to read it.
http://xs650temp.proboards.com/index.cgi?board=carbfaq&action=display&thread=731
Have fun! I am and its a great excuse to Ride!
Me and the Carbs know each other very well.