Hi Sam!
Tsumago and Magome are amazing! Do you plan to walk the old Edo path?
Tokyo - Magome
Magome can be reached best by bus from Nakatsugawa Station (JR). Here is an example route. It takes about 196 Minutes and ¥ 12,150 (if you don't have a JR Pass).
Tsumago - Takayama.
First take the bus to Nagiso station, from there it's 220-260 minutes by rail depending what trains you are traveling on. Here are some examples.
Travel to Koya,
From Kyoto station, take a train to Osaka station, from where travel to JR Namba station. Here is an example route. At Namba transfer to the Nankai express which brings you to Gokurabahsi (the station from Koya). Thispage gives you more information on how to access Koya. The route all together will take at least 2.5H. Note that the Nankai express is not covered by the JR Pass.
Kumano Sightseeing and back to Tokyo
Kuamo is more a region that one place you can visit, it is located closely to Koya and it is not difficult to access. However sightseeing spots are spread throughout the area and thus it is hard to give you detailed route information. I would suggest taking a look at this website which explains how to travel around Kumano. When you travel to Tokyo the best way to to travel to Kii-Tanabe then via Wakayama to Shin-Osaka from where you can take the Shinkansen to Tokyo station. Here is an example route from Kiitanabe to Tokyo. Travel takes about 330 - 350 Minutes.
Note that time tables for April 2014 have not been published yet, so times may have changed a little by then.
I hope this helps!
Daniel
