Hmmm... What to do.
Personally I prefer that the HDs and the PSU stay in the same chamber. They are easy to cool and are fairly tolerant to high temperatures. One low speed 12cm fan at the front and one low speed 12cm fan at the back should be more than adequate. Modify the front HD cage to accept your 5.5" tray and you'd be good to go.
If you are going to run 3/8" get a Swiftech Bayres/pump combo. It will save space and is very efficeint. I'm running one myself. I'd rip out that extra HD tray in the top portion of the case and mount my radiator there. The area is porbably large enough to house a PA160 or a single HC. If you tear out a couple of the 5.5" bays you might fit a dual BIP up front.
If you go the PA160 route you could cool the top compartment with two 12cm fans. I'd fiddle with the rear and top mounts to get your best temperatures. If you go with an HC and decide to stack two fans, I'd use both 12cm exhaust fans. If you squeeze a dual BIP in there , I'd also use both 12cm exhaust fans.
To tally up the fans....
With a dual BIP you would have 6 12cm fans, as you would with a HC with a stacked fan arrangement. With a PA160 you would have 4 12cm fans. For low noise the latter would definately be your best option.
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