Ok, all you need is two 1mm thick spacers with 32mm outer diameter and 25mm inner. Put them on the outside of the bearings on the new Gen wheel ('00-'03) and it will fit right on. You don't need spacers for the calipers, just pry the pads apart a bit before mounting and they'll readjust themselves.
I have a set of '03 wheels on my track bike (for slicks, have rains on the stock rims). What I did was to contact a KTM dealer and order four of these:
Washer 25x32x0.5mm
(two 0.5mm washers in each side). 25x32mm washers are a non-standard size, but they are used in the KTM 85 SX gearbox, so they do exist. Exact fit and you won't have the hassle of manufacturing.
If you haven't found out yet, the rear will bolt right up with the new Gen cush drive and spaces.