Something that might solve your issue with the kydex scuffing the blade(s):
Before you mold the kydex to the knife, cover the blade/guard/and whatever portion of the handle may fit inside the sheath, with a couple of layers of masking tape. It gives that extra couple of thousandths room, and keeps the sheath from scuffing the blade.
In the locations where the kydex "grips" the knife, you have to design the knife with using kydex in mind...that means using materials that will withstand the kydex rubbing on it, and also creating a knife profile that lends itself to easy insertion and removal from a kydex sheath.
There's a lot more to it than just taking any knife, and deciding you want to make a kydex sheath for it. The knife, the materials, and how the kydex sheath is designed all play a part.