I don't know how to do it with LimeWire, but setting this up would be trivial in Phex which also connects to Gnutella (and is written in Java, too):

Just set the incomplete directory to your stick in the startup wizard (or the directories pane in the options).

Phex doesn't buffer downloads in temp, but into ram, and you can adjust these buffers in the Options File, if you want to go into details.

-> Phex - Home

You could also try if just using Phex can reduce the stress on your disks.

Besides: Thanks to Sleepless for pointing me here.

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