@swatski - I took measurements prior to putting the boat up for the season and looked at all of the different options. I considered a dual 3700 gph centrifugal pump system (one fill, one empty) with electric ball valves and impeller pump primer all controlled by an arduino. I also considered using flow meters or timing logic in the controller to automate the system and display everything on a touch screen. I even looked in banjo pumps just because I wanted to compare.
In the end I have decided to go with the simple multi impeller pump and rocker switch system when I finally do my install. The ski locker is ginormous and I did find a bag that will fill it which will be great for wake boarding wakes when full. I came to the same conclusion as you on the side sacks so those will be 400 lb sacks. Lastly I will plumb quick connects for a swim deck bag. So 4 bags, 4 impeller pumps, and 4 rocker switches. All bags except for the swim deck will be vented. I have not settled on the intake(s) but that will either be a single 1.5 inch or multiple 1 inch for me.
On the inflating with air to reduce engine noise front you could always try a tube inflator with the bags to see if that works.
It will be a while before I get around to mine with lots of competing priorities for me this year so I am looking forward to seeing what you do.