I noticed these act as large ducts drawing air out of the engine bay also didn't realize at first as the hatch overhang conceals them and helps keep water out.

999JAY ... are your exhaust water cooled (IE: jacketed) thanks

Yes, there water-cooled a large electric pump pushes water into the lower section of the exhaust and the water exits the top and then goes overboard via skin fitting in the transom.

G is using a wrap (see image right side) so heat is prevalent,

the rudder water throw forward is certainly a concern but IMHO could be solved by adding/extending sheet aluminum just like is in place near the rudder currently

not sure if it is easy to see, but there is a triangular sheet of aluminum in place forward of the rudder, as a buffer in the rudder frame, extending it forward to the transom maybe a good improvement/modification, thus keeping intense spray off the transom area and air vents while getting up on plane

Overall do you think the swap from #6 to BPMs is going to be worth it, I would imagine annual maintenance is going to be a lot lower and efficiency is better.
With regards stability, the BPMs seem to run a lot looser but I suppose that's to be expected with the reduction in drag over the SSM

Seems Jay, as you stated many many positives. Boat "is a diff. boat now" at slow speed steering response slow, but all rudder boats have that trait, unless the boat has twin rudders directly behind the wheels. My question to you would be since your set up turns "in' might that be a good change for the 46 Skater to create bow lift, 90% of surface drive boats with a long set back spin "in" rotationally. a few images below, that do create vector force from the wheels. Thank you.

example of, twin rudders, behind the props

another, twin rudders