1. Any motherboard that is at least a year or two old should work fine, alternately you can check some of the Linux hardware reviews on Phoronix
2. If it's to be a Server: Suse EL, Centos, Debian - would be my choices not necessarily in that order due to personal preferences.
3. More RAM is always better.
4. I don't know .. maybe a place to start -> http://www.cobug.com/cobug/docs/database0034.html
You could always migrate the data to a SQL database no ?
hopefully someone else will be along with a better answer for No. 4