My dual 1.42 at work is currently at 57.4C. It does have 5HDs in it though.

5.25" devices will work just fine with the hardware from 3.25" enclosures. Its no different really. Its the pre-built ones which tend to have restricted firmware and will not allow the use of other makes or models of drives in them.
If this thing is going to end up as a 4U box, surely thats enough room to fit expansion cards without the need for risers?

Ah yes this one doesn't need risers hence the 4U, because mainly I'm not sure how to alternately cool the chip in some more compact fashion, and the heat sink is just shy of 3U.

However, this is merely the first one thats being done. Shortly I should have enough logic boards to make three of these, so it's more of an evolving project if you will.

Its good to know where I can get them from for the subsequent versions, and also if I can get a much smaller heatsink solution then they will very likely be adapted into this one at a later stage.

heatsink....watercooling?

Watercooling might be overkill. Or it might not. The G4 Xserve also uses the exact same CPU modules as the MDD, its just that they only shipped with 1GHz or 1.33GHz single and dual chips.
My point is the Xserve had a much smaller heatsink. Though it has much faster fans. And they never got to 1.42GHz for a good reason I suspect.
My (currently) single 1GHz Xserve is only transferring files from the network to its drives, but its at 29C. Thats pretty cool. I reckon it'll be happy with its new dual 1GHz module. It should be practically freezing going by the noise of the wretched thing.

So, if I fitted an xserve heatsink and stepped up the fans instead I could lose some height? How much smaller are they? I can find the part listed but no actual photographs / dimensions.
To be honest I'm really wary about introducing watercooling. Its not like the system really needs it
as it is, its not overclocked or anything, and I know very little about it to boot.
more research needed I think

sorry penny just dropped, it must be tiny its a 1U server isn't it. Doh!

There you go.

It is pretty small. It also has a blower right beside it and a plastic air duct over the top. And blowers are loud.

I don't know how quick you want those risers, but I need to order some other bits, and it would save on shipping if you want them ordered this week.
Feel free to iChat me. just use my forum name as an AIM account or .mac. Always happy to hear from fellow modders.

57c isn't that bad at all for a dual 1.42

My Dual 1.25 usually hovers around 135°f (around 56°c).

It hit 58.4C before I went out today around 11. I should add it runs distributed.net's RC5-72 client, so both CPUs are at 100% 24/7 (It won't wake up if I sleep it due to a USB 2 PCI card, and for some reason it takes up to an hour to boot, but runs just fine once it has).