Hi Corban: I'll do the easy questions first then make a dent in the harder ones.
I've got a V2100b and there's a link to a basic pic of what my system looks like in the 2nd post in this thread. However, I'm thinking of moving everything into a V2000b--I bought the version with a door because I planned on having the machine sit under my desk, but the door is getting on my nerves so now I'm looking to relocate the box and eliminate the door (talk about expensive "mistakes").
I tried a couple of different searches under my name but I didn't find a good way to come up with the pics I've posted--if someone knows how to only get my pics, please let me know. But, I should have a build log up pretty soon, all I'm waiting on to "finish" this box is my G5 and a couple of cables that should be available from Performance PCs in early June.
Drilling into the top of the case to install a t-line (or anything else for that matter) is very easy. The aluminum isn't difficult to work with at all. I used a uni-bit drill bit for the Danger Den fill-port in mine, but a hole saw of the proper diameter would work just as well.
As for your setup: First, put the t-line before the pump, not after it--the water should feed into the pump's intake.
If you're looking to keep everything internal there really isn't a good way to get a dual 120mm radiator into that box. Using two radiators probably is your best option, but take a good look at the amount of space you've got between the rear 120mm fan and where the CPU is located on your motherboard. With my Asus board it would be one tight fit, if it fit at all, to get a BIX and fan in there without seriously interferring with the mounting for the water block on the CPU. You might have to go to a BIP which is .75" thinner.
The biggest problem with using two 120mm radiators is that you're increasing the resistance considerably if compared to a one dual 120mm radiator. Most of the resistance comes from the fittings and the "junction" (don't know what its real name is) where the fittings are attached. The length of the tubes in the radiator don't affect flow anywhere near as much, so having a double radiator is much more efficient since you would only have one set of fittings/junction. Have you considered mounting a double (or tripple) radiator outside of the box? I've seen where people have done this cleanly and if you search a bit you can probably find some pics.
From all accounts the D5 (MCP655) is an excellent pump so you should be fine there. But, with very few exceptions, water cooling the north/south bridge is a waste of time/money/effort so I wouldn't add these to the loop in the initial build. They can always be added later if necessary. BTW, which blocks were you planning on using for the CPU and GPU?