My, you ask a lot of questions!
From reading them I suspect that (through no faut of your own) you would not understand some of the answers. So, instead of addressing each separately, I'll try and give you some general concepts and suggestions where further info can be found.
High end air cooling is as good, if not better than, mid range watercooling. Stay away from any "prebuilt" watercooling, it will accomplish neither of the following, much less both at the same time.
There are only two reasons to watercool.
1.) If your overclock is heat limited (ie. you need increased voltages to clock higher).
2.) Quiet.
Perhaps you should get your system up and running and work on overclocking first, to see if watercooling is really required.
High performance water cooling and silence are mutually exclusive concepts. While there are good pumps that are sufficiently quiet, radiator performance is directly related to how much air is flowing through the radiator(s). Within reason, it takes a certain CFM (Cubic Feet per Minute) to remove a certain amount of heat. Whether that air flows through one radiator or through six radiators doesn't matter, except that one radiator will require very high CFM fans (and the attendant noise), while six radiators would be served sufficiently by much lower CFM fans producing much less noise. If you start looking at CFM/db ratings of fans keep in mind that 3 db = twice as loud.
As for case modding, it will probably be necessary, at least some additional holes for tubing and radiator mounting (standoffs).
Again, if you need extra cooling for your video card(s) to overclock further, or want to eliminate the fans for quiet, then watercool.
Heater corres are fine, except that they take a lot of air pressure (and hence higher CFM fans) than WC radiators.
As for NB, SB, mosfets, and memory, watercool if you need more cooling to overclock further. In all but the most extreme cases a WC'd NB is all that is necessary. WCing memory is a waste, just remove the heat spreaders and put a fan on the memory.
As for the best components, you have to determine how much heat you will be generating and then pick the components that will remove at least that amount of heat with the water flow rates and fan CFMs you will be using. Have a look at
Martin's Liquid Lab.
I prefer a T-line. It's much less hastle to install and, though slower for bleeding air out, you only do that infrequently.
Currently there ar no reasonbly priced (less that $500) flow meters with sufficiently low flow restriction. An option is to install a flow meter on a bypass loop so it can be valved into and out of the loop. Then you can check the effects of new components on flow rates while not having to live with the restriction of the meter all the time. But then flow rates never change. A simple "bucket test" (pumping from a bucket, through the system, and into another bucket and measuring the volume in the recieving bucket and timing how long it took to get that amount of water) will be sufficient if performed before the components are actually mounted in the case to verify that yoy are getting the flow rate for which you designed. Note that if you want a flow meter to just know whether there is/isn't flow, a pressure guage can do the same. There also are inexpensive flow switches that can be set up to only supply power to the system after the punp has started, or to cut the power if pressure (flow) stops. Flow monitoring is pretty much useless as AMD CPUs will shut off and Intel CPUs will throttle down on overheat.
A for liquid in the loop, distilled water and a bioside ---ONLY!
Jubilee clips, great. See if you can find some with thinner bands though.
Contrary to popular beleif, plumbers tape (ie teflon tape) is not a leak preventative. It lubricates threads so that proper thread tightening/sealing is achieved. The only place I've ever used it is on the threads of radiator barbs.
Ah! Leak testing. An inexact science. There are many methods. Some people even use air and a pressure guage! Persomally, I mount the motherboard in the case, then hang the CPU waterblock near it's final resting place(s), mount the blocks to the video card(s), but not the cards to the motherboard (keep then out of the way), fill the system and run the pump. After the test I mount the components. Some thing to keep in mind: Plain distilled water (w/o bioside) in non-conductive. A few well placed paper towels can prevent leaks from reaching components. You can always break a connection from a component that is near the bottom of the case for ease in getting blocks/cards mounted, and then leak test that connection again with the mounting completed.
I hope this helps get you started off in the right direction...