Here are some answers to your questions:

Q: Are the 2-d surface fields availabe from the surface files a subset from the
isobaric main files, since their names are the same?

A:Yes

Q: We noticed that there are 6 3-d variables for the isobaric main, and similar
variables from the native file. We believe the isobaric fields (Z, T, RH, U,
V, VV) are converted from the native file? If so, can the 3-d microphysical
fields (pv, qc, Qr, qi,, qs, qg, qin, tke) that are available from the native
file be converted isobaric?

A: Yes and yes. You can interpolate vertically in each column to the isobaric levels that you need from the native file for the microphysics and TKE variables.