What I have done so far
I will try to answer most of the preceding questions:
@Stewbronco - I misstated wing root faring; what i meant was the wing spar penetration through the side where there is approximately 1/4-3/8" gap on one side and 1/8" on the other. I used pink styrofoam insulation cut to fit reasonably close and then liberal HT - RTV to seal and hold in place.
@birddog486 - see the below photos. A few dollars to have laser cut 1mm stainless steel (photo 1) and then bend ~90 degrees, wrap your exhaust pipe, and twist the "fins" to 90 deg so the the flow is not too restricted (photo 2)...works really good.
Photo 1
Photo 2
I ended up adding a second muff and putting 6 rows spread out on each muff because temperature is fine....but needed more volume. Now there is virtually no temperature issue, per se, except that the flap rod hole still puts a cold knife in you when the OAT is -53C (yes did that once over WY on the way to Mexico!)
@dpansier - what you describe is what has worked best so far. I took fairly thick marine vinyl and made a "pocket" for the arm off the torque tube to tavel inside of while bonding to the floor and side wall of the fuselage...which has been OK, though there is quite a lot of pressure to contain and with the relatively large area the glue will not hold for more that 2 seasons. The pressure created when flying is far greater that the "blow" my shop vac can produce when I duct taped the outlet to the hole in the fuselage ground testing for leaks and any constraint on the flap actuation mechanism. A pure bellows is not feasible as you have to connect to the bottom and the side of the fuselage, though it would be nice if it was just a round hole then one could do like the aileron push rod boots.
@pilotjohns - ideally sealed up or down, but as you say 99% of the time is up, and certainly that is the worst when at altitude and speed as opposed to the <80kts when the flaps are out. Are you thinking something 3D printed that covers the hole and is attached to the pushrod in a fixed location that seals when up?
Please keep the ideas flowing!