Thanks for the photos....

Before I say anything on the aircraft... engine trouble shooting rule #1
Remove the engine from the plane. Put it in on a decent test stand.

(you are an experienced modeler and may already practice this, but for the benfit of others reading...)

Controlled conditions - easy to see - easy to adjust - easy to make changes. Generally is more sold and stable than the airplane installation.
Run the engine. Keep it configured at first as it was in the plane. Same prop, spinner.
If it still misbahaves, check and change what is possible. Prop - plug - fuel. Change one thing at a time.
If it runs properly on the test stand, you have just isolated the problem - and the fault lies somewhere in the airframe/fuel system.

Something to consider based on seeing these, it was not clear entirely, but it looked like the tank is a fairly tight fit in there.

You should isolate the fuel tank from the airframe. Rubber padding all around.

Although you noted that you did not see bubbles in the fuel line while testing on the ground, it is not impossible that, in flight, the harmonics can cause the fuel to agitate and create foam in the tank. Once foam appears, the engine will go lean, and there is no two ways about it. Once those little temperature spikes hit the engine.... it is just not going to run right.

In my experience trouble shooting engine issues, over 90% of reported problems were traced back to the fuel system. So that is usually the first place I recommend that folks look. To this point, you have obviously followed that fault path per your photos and descriptions... as you have specifically check many elements in the fuel system.

That might not entirely be the problem, but it is good practice to isolate the fuel tank.

One thing I would do first --- remove the exhaust extension. See if that makes a difference. Sometimes, under the right conditions, the extension can act as an inadverting tuning device as it hits a certain frequency (rpm). This can cause surging. Yeah, its a long shot, but by far the easiest thing to try first.

Second easier thing to try, or at least worth an experiement.... change to a different prop. Unload the engine a bit and see if it happier. Two blade 11x7 would be a good start, then perhaps try a 2 bladed 12x6. A bit less load, and the engine will respond differently to each prop as it settles into an rpm range.

Let me leave it at that.... let me know how you make out.

Bob