Will it all fit? Good question. The three hard disks and DVD/RW will fit, but the water cooler would depend on which one you went with, size of hoses, size of Radiator, etc...
Wish I could help on board recommendations, but one thing I've run into building Aria boxes (the AMD64 will be my third box) is that finding m-ATX motherboards that have a full feature set (SATA/1394/1GB NIC) is tough. Even the MSI has only a 10/100, and most don't come with 1394 or 1Gb NIC for the A64 platform. You have to make some consessions besides only 3 PCI slots and two ram slots. This board looks good: GIGABYTE GA-8IG1000MK
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Wish I could help on board recommendations, but one thing I've run into building Aria boxes (the AMD64 will be my third box) is that finding m-ATX motherboards that have a full feature set (SATA/1394/1GB NIC) is tough. Even the MSI has only a 10/100, and most don't come with 1394 or 1Gb NIC for the A64 platform. You have to make some consessions besides only 3 PCI slots and two ram slots. This board looks good: GIGABYTE GA-8IG1000MK
-E