Tim, I looked at the logs with the pitch bobbing phenomenon. Lot of variation between desired and actual pitch, which is to be expected with soft rate PID's. But looking at the RC out, to see if the elevator servo is actually driving the tail bob indicates it's not. Classic indication of headspeed being too low.
Most Align helicopters won't fly very well with blade tip speed much below 425 ft/sec with a two-blade rotor, which is 1,450 rpm for your 800 stretch.