Could we get pictures of the deposits?
Edit: Since you can see the deposit, from the intake side, of the manifold, are we actually, talking about what I call, the back side of the valve head and not the combustion chamber side?
When I was a mechanic, the normal cause of a heavy build up, with umbrella seals, was loose valve guilds. Intake guilds shouldn't be looser than .0025. So, I would check both the guilds and be sure your Viton seals fit the valve stems. But, I wouldn't expect, even at .003 that the valves would have a heavy build up, in such few miles. So I would check the ID of the guild and OD of the stem, too.
I would also check the fit of the intake gasket for any sign of leakage or misfit.