Performing gage R&R study in R w/more than 2 factors

I believe that you need to consult a local statistician, as there are
likely way too many statistical issues here that you do not fully
understand. Alternatively, try posting to a statistical list like
stats.stackexchange.com, as I think most of your issues are primarily
statistical, not R related.

Yes, you are correct. I've actually been working with a statistician
within my organization, but the dilemma is that he's a stats guy who
knows Minitab, and I'm a software guy who's trying to deploy some tools
that are dependent on R. I've basically been trying to match up the
output of R with the output of Minitab to check my work.

Matt