Todd, do you have dhcp server running (on nt server)? Maybe that would be better? We actually used kixtart to nuke manually entered dns servers so dhcp could push down current/correct ones. I'm curious...If you use more than one client/protocol, be careful, those 000n's are created pretty much randomly when you add/update a protocol or client (I've seen up to 5 or 6, skipping numbers, whatever).
You might want to nuke everything under nettrans and replace it with a standardized configuration, so your script can find what it's looking for under nettrans/0001 etc.
You might want to set up a machine as dhpc client and check the registry, and then set it up with everything typed in manually, and compare the resulting registries. Then you'll know exactly where to put what you want.