I agree with Jobob (imagine that!) that the ultra cycling website is a wealth of good info. Also, there's a book called Long Distance Cycling that has tons of good stuff too.

I've found that you really need to do a few long, long rides to work out problems. I've done countless centuries, and a few really long rides. I have a bike that I've used on those centuries and a weeklong tour. But, on my first 300K on that bike, my knee started killing me at around 115 miles. Did more centuries on it no problem. I did a 300K on a different bike, no problem. Tried a 400K on that bike this weekend, and at around mile 175 the knee problem started again. (Had to DNF after 200 miles. )

Moral of the story: a bike that's fine for 100 miles might not be for 150, 200 miles. Same applies for saddle, shoes, shorts, etc.