Webpage says scaleable HyperTransport and different Gigabit Ethernet (i.e. Marvell & 3Com). Only thing I can assume from the scaleable HT would be that the K8V-D can change HT bus frequency from 800MHz and lower(600, 400, etc.) while the K8VSE-D can't but it's only my guess.
1003+ would be for the K8V Deluxe.
Dunno, maybe there are different voltage adjustment options or another for why it's better on OC'ing. Since the K8VSE-D didn't come out too long ago I suspect that the K8VSE-D BIOS, the one that comes with the motherboard, is pretty much up to date.