You're battling with the famous 500 flat spot....it was still there on the 650, as I recall.
One suggestion comes to mind, as I didn't see it in the posts I've had time to read:
Have you tried running with the airbox in place, but without the foam filter? (Like, with a paper or K&N or no filter at all?)
And, a comment: the 500/550 bikes always suffered a flat spot in the 4000-5000 RPM range for several additive reasons:
1. Long intake tract. This improved bottom end, but impedes the transition to high end until ramcharging occurs from the length, hence the "spitback" range, as we used to call it.
2. Poor construction of the intake tract right over the intake valve(s). This area needs a pocket, which reduces the flat spot noticeably.
3. Spark advancer rates never matched the cam on these bikes. To smooth out the flat spot for our lady riders, we used to cut off 1/2 to 1 coil on each spring: for the hotrodder we installed softer springs. Either one blended the flat spot into either an extension of the low end (cutting springs) or started the HP sooner (soft springs). Another option was to alter the cam timing, which accomplished the same thing: move it forward to improve midrange at the cost of 1 HP or so up high, or move it later to push the spitback range up toward the ramcharging end of the intake dynamics. This made it a Johnny-come-lately on the HP, but made an extra 1 HP or so at 8500 RPM, with power starting just over 6000 RPM. The change was 3-5 degrees on the cam sprocket.
Make sure on those carbs: the air passage from the air horn to the emulsifier tubes must be VERY clean. These collect tiny particles over the years, and are invisible to the user: this is the little brass fitting in the air horn that has a tiny hole in it: that hole goes thru the body to the emulsifier tube, adjacent to the needle jet, right at its base. Even a 25% blockage can cause uneven carb performance. I clean these with mechanic's wire and brake cleaner, then compressed air. Gotta disassemble the carbs to get at them (even remove the needle jet), but I've found it worth the effort, and do it to every bike I rebuild.