Gamma123,
1) seems a tad thick but should work as you have it. Making it thin will help keep the weight down and the energy required to move it. I think that is why most of the very low LTD engines are made that way.
2) the material for rods can be just about anything, light and stiff enough is all that is required. The bearings at the rotating ends are the most important. You can use simple holes with pins but make sure the fit isn't too snug. A small ball bearing is best but more difficult align correctly. Remember side loads, they will give you the most trouble with any binding issues.
3) I only made a guess at the volume difference in the engines I have made and ten to twenty times smaller should work for a typical LTD but be ready to do some tweeking for best results. There are formulas out there for proper volumes etc. Frankly, they mostly go over my head with the math involved so I size up my volumes from a best guess by observing working models I've seen. Not scientific and not the answer you want..sorry. Brass is easy to work with because it's soft and has low friction properties, also it's widely available and can be found in the sizes you already need.
4) I would use some kind of epoxy or simply use silicone to bond those together, your working loads are very small so nothing needs to be all that strong. A bead of silicone is quite enough I would think. A first working model isn't very pretty, leave that to the engines that follow and allow time and experience with the materials you find that work best.
5) Graphite would be my choice but I can't produce my own. I have purchased cylinder sets from
http://www.airpot.com/ but this won't be an option for this engine and your time line. you can use nylon spacers turned to fit your cylinder with a drill and sandpaper (works, I've done it) Others have "cast" theirs from epoxy by lightly greasing the cylinder and pouring in enough epoxy to use as a piston. You can even add the connecting rod end in the epoxy. You can machine a piston from aluminum, brass or steel if you have a lathe but the fit is critical and skill with a lathe is required. I don't know of any wood (balsa) pistons that work but it's possible I suppose. Fiberglass, yes, the epoxy anyway. I don't think it needs any reinforcement glass for a small piston. You can even try a balsa piston coated with epoxy and turned down to fit your cylinder I suppose. As for any explainations to your professor, I would have to say "material availablity and difficulty to work with to produce a working model" and not so much what the best possible materials really are. You could mention what the ideal materials are but explain the cost and or difficulty in using them for your example.
6) keep searching the net for other Stirling engines to examine and learn how they were made.