Gordon,
The push-pull design should provide a significant reduction of the 2nd harmonic.? The second harmonic seems to be an issue for 40 and 20 meters.? I would look at the driver and finals to see if there is an imbalance.??
For the 20-meter 3rd harmonic, I would check the LPF switching circuits to see if the diodes select the correct one and isolate the other filters.? For another issue, Ashhar Farhan suggested increasing the bias current for the pin diodes.? I'm not sure it is the issue here, as higher bias is needed for lower frequencies (due to the junction charge draining too quickly at low frequencies).
Happy Hunting!
73
Evan
AC9TU