a few suggestions :
supposing that all EDA tools, ported to x86 linux, DO work (with some caution, as mentioned above, with glibc, etc, etc.) :
choose a very simpel sound card - like creative AWE32/64 (if you have still have a free ISA slot) or PCI-128.
choose a standard graphic card - like nVidia TNT or similer ( GForce and above will need some kernel module compilation, wich may be complicated, if you dont know the tricks.)
choose a standard NIC - like RTL 8139 or 3COM's 90x series.
choose a simple optical PS/2 mouse.
perhaps, there is nothing new i have written here, but, just some guidlines.
you can spend as much time as you want with re-building the kernel for new soundcard / vga-card / usb-mouse etc.
it's complicated and time consuming.
if you want to build a dedicated linux box, i would strongly recommend you to use as much standard hardware as possible.
it will make life much easier.
regards