Okay, let's cover a few things that I know, not what I don't:
1) The engine isn't what needs to be at the 1/3rd up from the transom, that's where the boat needs to balance. Moving the engine forward or back is a way of achieving that balance point.
2) The shaft can be cut, but there is something you need to be aware of if you do so:
If you go with a square drive, the shaft can be cut but to do so means you will have to solder/weld on a stub shaft which can be very difficult for someone that's new to boating as length must be within a specific tolerance and welds must be almost flawless
If you decide to go with a round collet drive, cutting the shaft won't be as big of issue, but you need to be sure to cut the shaft long so you can adjust the length.
3) The most common location used for a radio box is just forward of the transom. The reasons for this is that it cuts down the length needed for the rudder pushrod(helps prevent bending) as well as keeping the weight as far to the rear of the boat as possible