You are on the right track - the carrier frequency change is done by selecting a different value in the C code for the RF Module init - others can probably point you at the required files.
The group number is a purely packet encoding convention - nothing changes about the physical parameters of the TX/RX packet.
Search on RFM12 over at jeelabs.org if you really want to dig some more.
P.S. It might be worth trying the original remote for the SPDIF switch - the cloned signals from the Harmony may be a poor copy.