From your description it sounds like the interconnecting shaft is not adjusted properly. Loosen one or both of the clamps on the small fingers at either end of the shaft. Back out the idle stop screws until they have no influence on the throttle shaft. Advance the screws until they just touch the bellcrank on the shaft and then advance another 3/4 turn. Now adjust the fingers on the end of the interconnecting shaft until they just touch the ears of the throttle shaft link, and then back them off to give about a 1/16 clearance. Tighten the clamps. Start the engine and operate the throttle linkage by hand at the firewall. Don't pull up on the turnbuckle at the manifold end, but use the link at the firewall end only. If one piston rises more quickly than the other, increase the clearance on the finger of the carb whose piston rises quicker. You'll have to fiddle a bit with the finger adjustments. Be sure that when you are done, that there is clearance when the linkage is in the idle position. Final balance is done with the stop screws and a unisyn or a piece of hose to your ear. Mixture and timing don't affect piston movement. Dirty chambers, bent needles, bent damper rods do, in addition to misadjustment.
Sometimes the taper pins that hold the horseshoe shaped throttle shaft links to the shaft wear out, and if that's the case, the shafts should be replaced and re-pinned.
If you need more assistance, write me from my website at www.sucarburetors.com
Rhys