I'm also about to build the BUSA 1/4 Cub with Ryobi. I've laid the motor on the plans and it of course will require moving the firewall back two inches to accommodate the mount which encloses the rear carb. As to which shaft, I've the short shaft and I'm not sure there is an advantage either way. The short will work.

Even with the magneto, the only thing extending from the cowl looks to be the last half inch of the spark plug and of course the plug wire but on the bottom it won't be very offensive. The spark plug is not a large one and there is a little more than a half inch of porcelain between the wire boot and the plug base so if a shorter plug is available, it might be that even the plug would be within the cowl. It wouldn't take a very big fairing added to the cowl to cover the plug.

The exhaust stack will exit the bottom of the plane aft of the cowl and if too much exit ventilation existed at the spark plug... it might not ram enough air back to ventilate around the exhaust stack. This of course can be dealt with.

I went with the fiberglass cowl with motor appendages.

I"ve dealt with the argument about 4 stroke sound with the Cub... but I'm wanting both fuel economy and far less exhaust oil.... plus, the Ryobi was on hand and cheap.