Wow - I know you can quickly get into trouble by modifying a motherboard but...

1. Put a 90 degree "bend" in the ATX connector.
2. Same but in the opposite direction for the PCI connector (+ an alternate PCI to AGP).
3. Maybe even remove or redistribute the USB/Ethernet tower.

... and that laptop would only need to be half as thick. Still, well done for making a MorphOS laptop!