"Now lets look at the intake side...."
Did I read correctly and you are suggesting everything should be smooth???
If so, this is an old school belief and absolutely INCORRECT. The engine may be basically an air pump BUT the intake port is going to flow both FUEL and air and since fuel weighs more than air it is difficult to keep it evenly mixed with the air as it follows the contours of the port. If your intake is smooth, the fuel will bead up on the walls of the intake port instead of staying suspended in the air. Rather than polishing the intake, 60 grit sandpaper scratches that are at a 90 degree angle to the flow is highly recommended.
Other than that (and maybe I just misunderstood), your writeup is great!
Heck, while looking at the intake side consider high velocity intake porting. You can do it yourself following MotoMan's easy to follow instructions - search the internet and you should be able to find them on his MototuneUSA website. The 8V intake ports are too big which causes blowback during the Charging phase; they would greatly benefit from high velocity intake porting. I suspect the same is true for the 16V but have never torn one down.