Given that you want low noise as well as good cooling, I would probably make my first choice to mount the rad at the front of the case pulling in cool air from the outside.
Fans inside the case will make less noise, and the cooling will be best using room air instead of air that has already been partially warmed by going through the chassis. (but the chassis cooling won't be noticeably hurt...)
Given the components you mention, what I would probably do is put the BIP on the front inside, with no fan in front of it, then put the 120 X 38mm Panaflo pulling through it via a 1-2" deep, tightly sealed shroud. I would NOT use a push fan in the front of the rad since front mounted fans are big noise generators (since there is a direct path from the fan to your ears). That and the PSU fan might be enough to cool the system, if it isn't I would add the 120 x 25 mm fan to the back of the case as an exhaust fan. (if doing this, seal all other case openings)
In either case, I would also remove ALL stamped steel intake and exhaust fan grills, and make sure there is a good free air path to the intake side of the rad. If you are worried about pets or baby fingers, use a steel wire grille, otherwise leave the holes open - this will minimize noise and maximize airflow.
Also pay attention to decoupling (rubber mounting) all fans, HDD's, and other moving bits. You might want to check out the Silent PC Review (SPCR.COM) website and forums for more details. This is the best cooling site, but they are the "Pro-Cooling" of low noise.
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As along as I have the Tundra bay res higher in the box than the other components does the orientation of the BIP's barbs (nice alliteration eh?) matter? In other words can I have the rad on it's side or tilted (if mounted in the lower front location) etc. w/o any major consequences and prevent trapping air in the it?
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Yes, it makes a BIG difference! You should make sure the rad output barb is at the highest possible point, on the rad so as to avoid trapping air in the rad. In general you should try to arrange the coolant flow to be as close to straight up and down as you can, avoid loops where the coolant line goes up and then back down, as any loop can trap air and trapped air will do really bad things to your cooling ability.
Also make sure to use a LARGE hose between your res and the pump intake if they are seperated. It is very important that the pump not have to 'work' to get it's intake flow. (Assuming the rest of the system was 1/2" tube, I would make the res -> pump in line 3/4" tube, preferably reinforced so it can't collapse.)
Good luck,
Gooserider