1) I have a YY cube, radeon 9700, and the danger den gpu waterblock as well, but there appears to be plenty of room to route the tubing over the card without modifying/replacing the fitting that came on the waterblock. I haven't actually put all this stuff together yet since I'm modding my cube right now, but I find it interesting that you don't think there's enough room to do this. I think as long as you're using ClearFlex or Tygon tubing, you shouldn't have a problem.
I was planning on putting a "Y" splitter in the line and letting the cpu and gpu get it's own supply of water without being pre-heated by other components, and then recombining the two on the output side.
You haven't mentioned which pump you'll be using.
2) On the hard drive cooler, I was also going to do that, but I couldn't find any commercially available hard drive waterblocks made from copper.
3) I'll be going PUMP > RAD > RES > CPU/GPU > PUMP...
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