I am pleased to report my heater is now back together and working like new. It took around eight hours of work over three days, $600 in genuine Pentair parts, and about $150 in new tools.
If you had all the parts and tools and no broken stuck bolts the repair could have been done in under four hours.
The Manifold Replacement instructions contain this warning to be careful once the bolts are removed to not push the tube sheet into the combustion chamber.
To get the stuck bolt out it took some drilling and then tapping the threads to clean it up and take a new bolt.
I was concerned the work risked pushing the tube sheet into the chamber which would complicate things.
I bought some nuts that fit on the removed bolts and used them to secure the tube sheet from moving. Pentair should recommend that in the instructions.
With the heat exchanger tube sheet being secured, the stuck bolt was removed, and the area was cleaned as the instructions specified.
From there it was all downhill, installing the new manifold and torquing the bolts. We went over the bolt sequence over a dozen times until the torque wrench clicked on every bolt.
Got the heater back in place, and reconnected the electrical wires, gas line, and water pipes. Started the pump to get water flowing through the manifold to check for leaks. Oops, needed to tighten up the thermal regulator cap and drain plug.
And then as
@Lake Placid warned Pentairs QC was not perfect. There was a drip from the 3/4" drain plug on the side. Wrenched that out and saw that the threads were hardly wrapped with Teflon tape. Removed Pentairs tape and put two good wraps of Telon tape, reinstalled, and no drips.
Time to flip on the breaker, power up the heater, and see if it will light.
Pushed the buttons, the control panel lit up, and I got SERVICE HEATER without the blower starting.