This is amazingly similar to the process I'm currently going through. Only difference being that I'm using a breakout board from sparkfun for the DS1307/crystal/battery combination.
My understanding was that there are inbuilt pull up resistors on the pins used for the wire protocol so additional resistors are not needed.
As for running fast I haven't left my set up on long term yet so I'm not sure if I see the same issue. I'll try and remember to leave it running tonight and see what happens.
I would be curious to hear what you're working on.
Just for reference I'm using this product
though I don't remember paying that much for it. :-? [/edit]