Thanks for the responses.
Amos - Are you talking about Nijo-jo Castle, or the Imperial Palace? I've noticed some mixed opinions on whether the Imperial Palace is worth the tour, but that the garden is very worthwhile.
I've read that some people saw so many shrines and temples that they got a bit burned out on them. Hopefully I can decide on a big enough variety of things to see so that doesn't happen to me.
I'm pretty sure the Japan Rail Pass will save money over paying for the side trips separately, so I'll probably get the 14 day pass.
So what do you do on weekends to avoid the crowds?
Thanks again!