912 overheating after maintenance

My money is still on the new/rebuilt muffler.  Did you keep your old one? If so you could do a quick swap to see what happens.   

I’ve got a used muffler I can swap it with. Might need a few welds to fix the exhaust pipe. 

So, how can we assume that it’s not a water cooling system problem? 

The Plug Temps affect the temp of the Plugs, not the Heads.
if too Cold they Foul easier.  If too Hot the electrodes erode faster.

The exhaust Pipe wrap affects the Temp of the exhaust, not the Heads.
The more heat goes out of the tailpipe, the less heat is dissipated under the cowling.

A properly operating cooling system will purge all air naturally.
The Pressure (Radiator) Cap on the expansion tank should be the High point in the system.
It will purge any air into the Overflow bottle and replace it with coolant from the overflow bottle.
The small hose from the Expansion Tank to the Overflow Bottle can be Clear PVC to monitor the Cooling system's operation.
This hose will get warm but Not boiling Hot under normal operating conditions.
This hose should ALWAYS be 100% full; Hot or Cold.
If this hose is 100% Full, so is your cooling system.

It was reported that the engine "Seemed to be running normally initially but 45 min into the flight was noticing the temp trending higher."

This would tend to indicate that "Something Changed" in the air.

Immediately prior to the problem, repairs were done to the exhaust and fuel system.
The ash on the plugs indicates that fuel delivery appears to be nominal but the temperatures may be on the hot side, but we already know that.
The final item that keeps getting ignored is that exhaust/Muffler that we just do not want to admit may be the issue.

I am with Jeff,  have a close look at that muffler.
It may be that a baffle didn't get welded or it wasn't noticed that the packing slip was stuffed in one of the pipes and is still in there,

Nick Asked;
So, how can we assume (Confirm?) that it’s not a water cooling system problem? 

Point an IR Thermometer at the Radiator.
If Coolant is freely circulating, the Radiator temperature will be very close to the temp reported by the heads.

If the system has a thermostat, you will need to wait for the T-Stat to open (>185°F).
Do not attempt to get an IR reading from bare metal surfaces.
This will result in False Low readings.
The radiator Header Tanks or the radiator hoses would be better sample points than the cooling fins unless they are painted.

Rotax Mechanic did a compression check and #3 cylinder was at 60 psi.

He said the exhaust valve is stuck and he thinks this was causing the overheating.

Any thoughts?