I am going next month, the Japan Rail pass sounds like a big saving, can I also use Shinkansen trains with the Rail Pass? Specifically the Tokyo to Kyoto route (JR central)?
Look carefully at it; probably you won't be able to use the fastest trains with the JR pass.
Also, if you're just going to Kyoto from Tokyo, it really is not worth it to get the pass. Just buy regular tickets. The pass is useful if you're doing a lot of train travel in a short time.
That's fine, but if you spend more money to go slower, that's just stupid. The point is that the pass is a really bad deal, or at best, break-even, unless you're traveling a long distance and within a short-ish timespan. Tokyo-Kyoto is not a long distance and isn't worth the pass at all.
Also, if you're just going to Kyoto from Tokyo, it really is not worth it to get the pass. Just buy regular tickets. The pass is useful if you're doing a lot of train travel in a short time.