Well, I still need to upload pics, but:
I went with an early KTM Duke hub for the front.
It's 17mm axle, and the KTM hub is easier to find disks for than early Bergs (yes you can modify a DRZSM rotor, I have one sitting here), and if you haven't already discovered, the original front Berg hub is a non-conventional spoke pattern. That makes it a PIA to get spokes made and rims to fit correctly. Not impossible, but you have to ship your hub to Buchanan's to have them custom cut spokes.
Instead, I just ordered a spoke kit (from KTM) for the duke hub and I'm lacing them to Warp 9 rims.
My local KTM shop also just happened to have a new Ferodo 320mm floating rotor that fits the Duke hub, and I got it for a song. He also had a relocator for a brembo caliper but it's the later wider bolt pattern for the fork leg, no biggie, I'm just gonna drill and tap a hole for the early mount pattern. Both the relocator and rotor have holes for mounting a Trailtech speedo sensor and magnet with retainer clip, respectively. It's like it was all mean't to be.
On the rear I used an SMC/any big bore KTM cush hub P/N 5841001034491, and picked up a sprocket carrier and rubbers of eBay. If you do use this hub note that there are 3 different sprocket carrier part numbers for this hub as the carrier bearings changed throughout the years and are dimensionally different. Depending on which sprocket carrier you use it may require a different width spacer between the sprocket carrier and the hub to keep the carrier properly seated when the wheel is tight.
Even though the P/N for the cush hub is the same for all years it usually ships with the later thin spacer, and you will need the order the earlier thick spacer. I used the earlier thicker spacer with a '95 sprocket carrier.
EliteKTM has an awesome parts fiche and I used that to determine which spacer I needed.
I also ordered a rear spoke kit for the SMC wheel (the earlier wheel that uses 4.25" rim) so I shouldn't have any problems lacing it up to a 4.25" Warp 9 rim.
I ended up milling ~1mm off the inside face of the rear caliper carrier where it mates to the hub. This gave me more clearance and lined the rotor up dead nuts in the caliper carrier. I milled about ~2mm off the outside of the caliper carrier and the hub dropped in. **BUT** I didn't need to do that. When I tightened down the wheel it seated the sprocket carrier in the hub more than I could do it by hand and when I loosened the axle the gap at the ouside of the brake carrier was about what I had milled off. No sweat, I just slipped a stainless washer in there to take up the slack.
Chain alignment is correct and the rear caliper is floating within range of the carrier and the brakes work. It was EASY.
I should have the front hub and spokes in the next few days so I can tackle the front brake setup and wheel spacing.
Then the rims should be in about a week after that so I can lace it all up.
I'll see if I can't get pics posted up today.