I think you are right about the cause of the "softness" of Jpegs. The anti-alias filter would affect everything and the NEFs clearly are sharper. As for the IBM microdrive, I have had the same concerns. I wonder what would happen, for instance, if one dropped a microdrive on a hard floor. Maybe nothing ....but on the other hand....? I am thinking now of getting one of the "digital wallet" type long term storage devices so I will not have to carry a laptop with me on long shooting trips. This is especially important as I am shooting a lot for stock these days and that means my F100 and lots of Provia 100F goes along on the trips, too.
After reviewing your message of a few days ago, where you outlined your shooting settings and workflow,I wanted to ask if you never use WB on auto? And, if not, doesn't that slow down your shooting a lot?