A quick Update.
Installed a new Thermal regulator (kit). The start up sequence remains normal. Approximately 5 to 8 seconds after the burner lights, the unit begins to vibrate and the "rock" banging begins - - but not to the extent previously noted. The temperature will increase a few degrees but not enough to shut the system down. The noise and vibration stop shortly afterward. The burner remains for a few minutes and then shuts off (normal operation). The burner will come on automatically several minutes later and continue the cycle.
I believe the rock banging noise and vibration is from steam being generated in the heating coils. With a new thermal regulator installed, the next culprit should be the Manifold bypass valve. On this early unit, the manifold must be removed to replace the valve. I'm waiting on the FedEx courier for the o-ring kit, which I want to install since I'm removing the manifold.
I believe the manifold valve is partially open and diverting some of the cold water from entering the heating coils. There is insufficient water volume/ flow to keep some of the water in the coils from turning into steam. I'm also suspicious that there may be air in the system. I recently installed a two speed Pentair 1 1/2 HP pump. I'm having a tough time maintaining a closed system (no air) especially in the low speed mode. I am NOT using the low speed side of the pump when operating the gas heater.
I'll update you as I proceed. Hope the manifold valve solves the problem.