Hi daniel1212,
Great post.
I saw no mention of a graphics card in your attempts to improve performance. If you are using on-board vid, it is probably sharing some of that precious and limited 4g of RAM... And the on-board is likely to be a 512mg card.
If you were to add a vid card, not only will you gain the RAM the on-board vid is using back to the system, but if you get a 2g vid card (off-brand should cost you in the $40 range), you will be astonished how much faster the machine will render to the screen. I believe you will see what feels like a 25% improvement on top of what you have already done...
Yes, it has a video card, and the custom made Asus made Sony board and PSU is very picky on what card will run on it. It says it is a ATI/AMD Radeon X300/X550/X1050 (RV370) [Sony] video chipset with just 128 MBytes of SDRAM Video Memory, and I tried replacing it a ATI Radeon X300 SE 128MB DVI VGA TV-Out PCI-E PCI-E Video but it would not work, and likewise with a couple others, but i do not want to risk spending more money.