Manuals specify 0.010" endfloat on mainshaft as stock. Hub is straight on shaft so same measurement. That's for both Scout and Chief. My Scout is running 0.024" with no problem.
When you did the clutch did you change anything else? Oil type etc. Have you had the bike out with the new clutch? How is she shifting?
How tight are you making the clutch pedal nut? Just seems strange that all you changed was the clutch pack. Maybe the whole setup just needs to settle in.
You might be better asking the question on the Virtual Indian mailing list. There's some proper old school experts on there. And they're helpful. http://www.virtualindian.org