Okay, here's the plan, for me anyway. Run with only the one RAM chip for a few days like everybody suggested. With all the problems you've had with it I won't spend anymore time unless you make sure it's stable with the one chip. I also would not recommend upgrading RAM and HD until you know it is stable.
As far as DW goes you're making more out of the directory report than it is. On mine I ran it and have 203,000 out of 1,561,000 items out of order. It doesn't mean anything is broken, the directory that holds the info where things are on the disk is just fragmented.
You can't "fix" the boot drive unless you boot off of the DW CD. With the small amount of RAM you have DW probably won't be able to repair anything anyway. It needs 512 minimum usually.
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