At the risk of repeating some of what has already been said, can I offer the following -
Prop shaft - first, make sure the threaded section is only just long enough for the prop and a locking nut - you don't want a threaded piece running in the end bearing as it will cause wear and might leak. Cut off any excess with a hacksaw, then file the rough edges off (and leave a nut on the thread when you cut, so it can be wound off to clear the thread). Wind a nut down to the bottom of the thread, then screw the prop on as far as you can. Then (Very Important) tighten the nut hard against the propeller. Put a washer on the shaft, then slide the shaft into the tube (having added a slug of waterproof grease as you have no oiler on the tube you show). Then slip a washer on the inboard end of the shaft, then the locking collar that Colin Bishop pointed you to. Tighten the collar so that there is a barely perceptible movement fore and aft of the shaft, then spin it a few times to make sure it runs freely. It is the locking collar that takes the thrust when you are in reverse. Then you can add the universal joint between the shaft and the motor. The UJ should not be subject to any forward or backward forces, all those are taken on the prop shaft tube.
Rudder - it doesn't matter too much if the rudder isn't right up to the hull (although some purists might point out that it works most efficiently when it is), but I suggest you cut off the collar that is supposed to seat on the hull and leave the end of the tube sitting below the hull at the distance you want the rudder to be. You will have to dispense with the nut that would normally be used to fasten the tube and employ a healthy dollop of epoxy adhesive to glue the threaded portion into the block it passes through. This will be perfectly watertight, and will stop the rudder riding up if there is a gap between it and the tube.
Hope that all makes sense. Good luck with your build.
Greg