Granted I don't know why you have both high idle and low i/o wait, but my eye is attracted to this part of your post:
"...and prints the line back out to another file on the same disk."
Is there any way you can have the input and the output files on separate volumes (or strings)? You might have faith in the machine's RAID setup (assuming there is one), but it's not guaranteed to save your bacon. Give it a try, even if the input (or output) has to be in a different part of a LAN.
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