John, this build is looking oh so good! I think from now on, I'm just going to shelve any conversion ideas and wait until Hasegawa releases the kit! I currently have the trainer versions and the A6M8 under way, and the devils released kits of both!
I noticed Hasegawa elected not to address the air intake issue in this kit. I have a book of engineering drawings of the Zero fighter, and one shows a Y shaped intake plenum on a Zuisei engine installation. I modeled this by filing two rectangular slots in the upper lip of the cowl, about the 10 and 1 o'clock positions, then boxing them in with styrene. These would lie just outside of the gun troughs, and the plenum ran over the cylinders until it cleared the rear bank, then curved downward and inward to join into a single intake pipe attached to the carb on the rear accessory section so as to clear the gun troughs.
I think this kit provides you the option for a two-blade or three-blade propeller. From what I can find, they did install a three-blade on the Zuisei engine to combat vibration, but it is imposible to determine exactly when that occured in relation to changes in the oil cooler configuration and the anti-spin strakes.
But, ain't that the fun of modeling a prototype? By definition, the thing changes appearance almost every day as the flight test data comes in! By the way, love your builds, you are indeed a skilled modeler and it's a pleasure to watch your work!