Firstly, you would have known it by now if that much primary oil went into the cases... Plus, as pointed out, this is totally unheard of - some few early Evo's had casting issues in way of the sprocket shaft case insert, but that lead to leakage the other way round.
Secondly, just curious, why did you take the inner primary off to replace your stator?
If you did, I have three suggestions:
1. Are you sure the large O-ring sealing the inner primary to the cases is good?
2. Could be a crack in your primary cover in way of the drain plug.
3. The jack-shaft is probably too high for any significant loss of oil, but your tranny input shaft (clutch out) is lower. Have you checked your belt & tranny pulley for any signs of oil? You could lose oil thru' there without noticing oil spill elsewhere.
Try this: Fill your primary up to the clutch spring as prescribed. Ride a few miles down a dry road, and ride slowly back carefully looking for any signs of oil.