After some deliberation I decided to use one of the existing risers, as I have no intention of using a separate graphics card I didn't worry about aligning with the existing slot holes. This also meant I only had to cut off one riser and install three.
I wanted to use as many of the original Shuttle components as possible, this included the original rear fan in its housing that would have contained the heatsink, I had to rotate it 90 deg to get the very short cable to reach the plug on the mobo.
The only issues were that one of the SATA power connectors had broken so I had to use a molex-SATA converter, and the internal USB connector for the front panel is just ever so short of the connector on the mobo.
I had to use extension cables for the 20/24 pin power and 4-pin power. The clearance over the memory was very tight, needed a bit of shuffling to get the PSU in place.
The back panel is a bit exposed, I need to alter the IO shield to make it fit which will cover it up a bit.
The original drive tray has a plastic clip underneath for keeping the cables tidy, intended for IDE ribbons, but works as well for flat SATA cables. The two black cables are from the card reader on the front. The nice aspect of the Shuttle was plenty of ways to tidy up cables by routing them over the frame and using the provided clips.
Plenty of space at the moment (relative to a SFF), I may consider getting an upright cooler if it is the right orientation and can clear the back of the DVD.
There doesn't appear to be a cooling problem, but I'll need to stress it before confirming, the only issue is noise, the stock cooler is like a jet plane and the rear fan makes much more than normal, this might be due to it being overpowered, perhaps turning on the fan control may work. I have a spare large (120mm?) fan and may fit on the rear instead if I can find some rubber gromits which could improve internal space.
Right now I'm a bit stuck as my edition of Windows XP Pro is pre-SP1 and doesn't recognise drives of larger than 130Gb, so I'll have to create a slipstreamed CD to continue.