Help locating bottleneck on new mining rig
Did you check the CPU usage? You can use TOP on Ubuntu (sudo apt-get install top, if it's not default). If it's not capping out at 100% it's either the chipset or CPU bandwidth giving up. You can also check you regular memory, although I'm quite sure that isn't used in GPU mining.

Some things you can easily strike off are network and disk. Disk isn't used at all and network shouldn't cap out even on dialup.

If it is in fact chipset or CPU bandwidth you have two options:
1. Overclock. Focusing on FSB clock should improve everything. I'm quite sure you can't get a 300% increase though.
2. Build a different system. I daren't advice about this though.