As far as how you get your eSATA ports, thats the same trick I use on my Mac Pro, little adaptor plate with cables running into the system to 2 unused SATA ports. Works great for the few times I've had eSATA drives attached. They don't get much use though as I prefer my NAS instead.

I can't tell what nForce chipset you have, but it looks like you do have one based on the NVidia reference there. Main reason I asked is that the I/O degradation sounds eerily similar to the failures I've seen at two companies using NForce powered Dell XPS machines. The difference here is the Dell's all used NVidia Intel chipsets, not AMD. The reason for the failure was a bad system design that dumped heat from the CPU directly onto the chipset. As the system aged when being used to compile code all day or sit in an office overnight without air conditioning, the chipset would just start acting oddly, usually slowing or delaying IO to the point of the machine being useless.

I can't say for certain this is similar to your problem, especially since it went away when you stopped using the eSATA port. I'd still recommend double checking the chipset though internally, make sure it gets enough cooling, and doesn't have a ton of dust and such on it. To identify the main chipset, it's going to be a component on the motherboard that has a heatsink on it, usually located somewhere near the CPU or memory. The heatsink may have it's own small fan, though the heatsink/fan setup will be much smaller then the CPU one.