Just a thought, you should try spellcheck next time. It is hard to read your post as it is... Just sayin'.

Now to the questions:

1) Shaft size is dictated mostly by prop size and what you plan to do with the engine. You need a smaller shaft for a slow, gentle flying WWI bipe than a balls-out aerobatics plane. I am a mechanical engineer, so I would size it based on the design loads and then add a fair bit to account for prop gyro loads.
2) RPM can be anything you like. You take the prop you want to use and figure out how much horsepower it takes to turn it at your desired RPM, then work back a reduction that lets the engine make that much power. You need an engine that will make the power at an RPM that will be reasonable for the prop, too. A bit of iteration is required here.
3) Prop size and pitch need to be determined first and then everything else comes after. In Hewismayer's case, he wants a 39" prop for his 1/3 Sopwith Pup because that is the scale size. So, that sets the diameter. To get the pitch, you need to decide how fast the model must fly at full throttle, then figure out what RPM that will be at and if your engine can turn that prop load at that RPM. You need to work back and forth to get a pitch that will fly the plane and that your engine can turn properly.
4) I would use sealed ball bearings for the shaft. You would need to check the axial load rating on the bearings to make sure they can carry the thrust load as well as the radial load.
5) Best test subject is an old, ugly, easy flying test mule. Save the nice scale plane for after you know your power system is reliable and has been proven.

Mark