I recently purchased a Midwest Aerostar 40 from a local hobby shop. I planning to make templates of the bulkheads and other parts that are not shown in the plans as to their size so I can perhaps reproduce them at some point. Just wondering if anyone has any hints as to the best material to make the templates out of?

I would probably not bother making templates of the parts at this point in time. Depending on the complexity of the parts, it helps greatly to have a scroll saw and a good disc sander. If it were me, I would either trace them on a clean sheet of paper using a mechanical pencil, or even just xerox them. The copied parts will have a shadow (due to the part's thickness) but its easily discernible and can be ignored when cutting new parts.

If you really want templates at this point in time, probably the easiest for you to work with would be a clear plastic material call See Temp.

X2 on photocopying. Many (if not most) home inkjet printers also have scan/copy capabilities these days and a color copy of the part is very easy to use as a pattern to cut a new part.

Get some 1/4" square graph paper and tape the parts to it, then scan and save as a PDF. You can correct for any errors in scanning using the graph paper as a reference.