Whatever you do, I would definitely get that system problem(s) fixed before anything else. If you are aware that your Mac is not running up to full potential, I would start SCREAMING.
Now one issue I can see, is that you have very poorly placed memory. You need to be very careful to follow the setup to insure that those 4 x512 modules are in so that they have 256 Bit wide access. The issue might be, depending on what at the bottom means; is that putting those 2 x 1GB modules first in the data flow path, most likely kills the value of the 4 x 512 modules in the 256 Bit wide setup.
it is my understanding that you need two of the 512's on top and two on the bottom riser cards in the correct orientation to gain 256 Bit wide access to RAM. The 2 x 1GB modules will never add much to that since they can only be addressed as 128 bit wide. You really need 4 identical sized modules - 2 in the top riser and two in the bottom to maximize you RAM accesses.
Now, with that said - the memory misalignment issues should not be causing the Beachballs of Death. I would suggest that first, run the Apple Diagnostic CD that comes in the box to see if it says everthing is OK! Make sure that you have run Applications>Utilities>Disk Utilities - and at least checked Disk Permissions for no problems.
But try to get the RAM installed correctly as well. The instructions should be in the manual that comes with the system.
And sorry, I didn't address the FCS2 questions. It all looks great.