I flew two more batteries and after some adjustments the CX2 fly great again.
I'm not sure what I did that fixed all of my problems but here it is.

1. I did not remove the ball links on the flybar linkage but I did reposition the links on the balls so that they are "more square" with the balls and rotors if that makes any sense. I just twisted them within the available range of motion.
2. I tightened the flybar holder screw thinking there was a little too much play in there.
3. I didn't notice at first but the new flybar seems to have caused the need to readjust the elevator and aileron trim tabs slightly more in the same direction they were previously set. Apparently the new flybar magnified the slightly unlevel swashplate.
4. I also lowered the motor gain pot to correct a slight tail twitch that has always been there.

My last battery was nearly perfect: stable hover, excellent control, continuous foward flight with a single forward control input and all the glitches and noises seem to be gone.
I guess the next step for me is to level the swashplate by adjusting the servo pushrod control links. Although it is still well within the trim tabs ability to correct. The elevator tab is just below center and aileron is slightly less than halfway between center and full left.
This never needs to be changed during flight. I am, however, constantly adjusting the rudder trim as the yaw changes due to what I believe is a heating up issue with the battery and motors as the flight progresses. This has always been the case and not a problem.

Check my thread here " CX2: CF Boom & Front 3rd Stock Tail" if you're interested in what my mod. looks like. Pictures are before I installed the Dynam Vortex Flybar discussed here.