The dohc design is a little soft below 3000 rpm- you will just learn to drive it a little differently than a small block vette. I give no quarter if and downshift into 3rd sometimes on the freeway just because there is still usable top end left on the powerband.
My last 95 coupe with the blue label ZF made the same exact noises- it is normal although it may vary from car to car. It can be tuned out with careful assembly and blueprinting, but I wouldn't touch it unless something else goes wrong with it. I do not believe the noise is an indication of impending failure or shortened lifespan. ZF's make all kinds of noises from the bearing whine to 'box of rocks' grumbles at low rpm lugging and such. Bill B (ZFDoc) has all the info on this box and his services at
http://www.zfdoc.com/.