CAT - I had a sudden thought: if your Shuttle genuinely takes FlexATX motherboards, then Via do
a couple of iDOT motherboards that might be an option. They only use C7 processors @ 1.5GHz, so they won't have stellar performance, but the higher spec one sports both PCIe x16 and PCI. The only real downside is that they support a maximum of 2GB DDR2 (2x1GB), but that's not a huge problem in a low spec system, I wouldn't think...
EDIT: Having googled up images of your Shuttle I don't think that'll work at all - while the motherboard appears to be flexATX size it runs the "wrong way", as it were...