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Mounting the rad on the top of the case is fine, although completely bleeding the system will be difficult. Since you have a 360mm radiator, you want ALL 3 fans one the same side of the rad. So a cross-section would look like: grill | case | fans | shroud (optional) | radiator. The fans will be...
1) Personally, I've had good experiences with Thermochill radiators. PA120.3's are a little expensive, but they are supposed to be some of the best. As for watercooling the chipset, it won't make huge difference and may just increase your CPU temps.
2) If you use 7/16" ID tubing over 1/2"...
I also have the PCP&C 750 Silencer in a CM Stacker. I had to invert my motherboard tray, so my 8-pin connector is in the bottom corner. My PSU is at the top, and the 8-pin cable wouldn't reach if I tried to route it behind the motherboard tray, so I bought a cheap ATX extension cable. If you...
PT Nuke is copper sulfate, and I have been running that in my loop for 2 years without a problem. A few drops of it is all you need.
As for your leaks, don't screw your barbs in too tight or else the O-rings will not seal correctly. Also, don't use plastic barbs, as they rarely work well.
I have two Thermochill 120.2's and I've found that separating the CPU and GPU's in two different loops provides significantly lower temps, at the expense of double the cooling hardware. However, since you already have the radiator, it should be fine if you're casually overclocking it.