@ carvedeye
I'm still contemplating this myself but struggling to find a decent looking yet not-too-expensive tower that is tall enough.
However, most ATX towers are in fact deep enough to mount the Amiga horizontally. When I finally get around to it, my solution will be to install the Amiga mobo complete with the lower half of the casing (which will provide the insulation). All the ports will be extended to make them available at either the PCI backplates or the area normally occupied by the ATX mobo's PS2/USB/Serial/Parallel/LAN ports.