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Re: Repair or Replace Aging Heating System with Gas Conversion Gun?
The draft regulator is not in the correct location. Get it serviced. Get a combustion report. Upgrade the primary control.

Re: Repair or Replace Aging Heating System with Gas Conversion Gun?
The primary control, shown in the last pic, is failing. One of the components in the flame-detection circuit has become unstable. We have a bunch of these burners in our customer base, and generally replacing that control with the current version solves the problem. The new version also has some diagnostic capability that can tell you why it locked out, can display the flame signal etc.
These burners run very well in W-M Gold boilers when properly set up, and I see no need to completely replace them.
I'd have a pro come in and replace the control, do a combustion test to make sure it's running properly, fix the leak on the fill valve or pipe above the measuring cup, check the expansion tank for proper air charge etc.
IIRC, the indirect tank is a re-branded Triangle Tube unit. The corrosion is coming from bad joints above the tank. Have them replaced and you should be OK.
Re: Trouble on the Roof
Many of you if you worked on oil have installed oil tank vent piping. When I was in business for myself I had an oil company call me because the driver had overfilled a 275 gallon tank and it bulged out and was leaking.
What happened was these two houses had a "community driveway" one driveway between the two houses and the driver got confused and started filling the wrong tank which was already filled.
Most vent caps either screw on a pipe thread or more commonly for a 275 they go on the pipe with a set screw and the vent cap has a little stop on it so you can't push it down too far.
Well, the tank that bulged had an old vent cap with no stop so it was down on the pipe with little room to vent. Never saw another vent cap like it.
It worked ok when it only had to vent air through the small gap but with the tank full it could not vent oil fast enough and it over pressured the tank.
Re: System 2000 - Bad Temp Sensor
With what @mattmia2 suggests above, this may work with a Thermistor type temperature sensor. By the sensor description provided above from the manual and also posted above (and now below), I believe this senor is not a common Thermistor type sensor. I believe the Sensor is like or similar to the DS10B20 type, which uses digital communications to report the temperature, not analog. If the Manager does not see coherent data from the sensor it displays an error.
Re: Magnesium anode vs Electric anode vs No anode
the floating stuff is magnesium hydroxide from the anode(or other salts of Mg depending on what is in the water). the iron in the water probably plated on to the steel pipe from the mg-fe cell
when you concentrate the minerals in the water by evaporating and adding more you increase the conductivity of the water so more current flows in the powered anode (probably limited by the power supply) and the Mg anode dissolves a lot faster from the hinger current and the unprotected pipe rusts faster.

Re: Magnesium anode vs Electric anode vs No anode
the iron only one isn't oxidized on the submerged surface but the surface is gone, it is raw iron where you piped it and that black stuff you dumped out is some oxidation state of the iron that dissolved. I think there is some iron in the water to begin with but not that much.
i think the black pile under the anode is particles of Mg metal coated in Mg oxide. The Mg hydroxide i believe is a slimy, white, cloudy gel that is slightly to somewhat soluble in water. If you add a lot of water it will dissolve, with a little water it forms a slimy precipitate.

Re: Trane Air Handler Fan Constantly Running
With an Air handler stopping and starting the cooling and the fan at the same time isn't a big deal. Usually on cooling you start the indoor blower and condenser at the same time. You can continue running the fan TD off but won't gain much if any efficiency.
On heating you usually delay the fan on start up so the occupants don't have cold air blowing on them it gives the coil time to warm up.
TD off on heating…same as cooling won't gain much efficiency.
TD off is more important with a gas or oil fired furnace. You should never shut the fan off with a ripping hot heat exchanger