The best possible arrangement here for Linux is:
0) Connect the two machines via a crossover cable and 100bT Ethernet cards (cheap used ones can be had).
1) Set up the main system on one of the machines with a minimal GUI that will rarely be running - this will be the "server". This machine should have the best hard disks.
2) Set up a second system mainly for running X with a full-featured GUI - probably WindowMaker.
3) Configure things to run on the main system but display on the X-system. You can still use the X system for storage but you want the other machine to do all the important stuff (servers and applications).
This is one of the main strengths of Linux, that is rarely exploited. You can isolate the GUI on its own machine. In fact the best Linux setup I ever had invovled an X server running on a Windows machine. The Linux machine did not even have a monitor, just a green-screen terminal.