For the timing to be slow enough to raise the manifold temp, it would also be having performance problems, loss of power.
You could try insulating the fuel line, getting it away from the manifold. Do not insulate the manifold, it needs to dissipate the heat.
An easy test for the questionable fuel cap, just loosen it, see if there is a difference.
I would somewhat suspect the inline filter. Paper filters are made for systems with a pump, not gravity flow. You might can find a screen type filter at a small engine supply. I have used the glass screw together type with mixed results, they are prone to leak.
The difference you are seeing when the PTO is on is the increased load on the engine. More load means more fuel demand and more heat generated.
About the coil, have you felt the coil when it fails? A normal coil will be about the same temperature as the surrounding components. If it's too hot to hold, something is wrong, bad coil or the wrong coil. Assuming this is a 12v system, it needs a true 12v coil or a 6v with a 1 1/2 ohm resistor. Many times coils are mis boxed. Either check the resistance across the primary terminals or go by the part number actually on the coil, not just by the box or what the counter man sells you.
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