Yeah but ipods don't skip!
Just a thought, the wireless FM modulators suck pretty bad. They make wired ones, that actually connect to the antenna of your receiver. They work better than the wireless ones, but can still only achieve the frequency response of the receiver, which is typically less than that of a cd or other digital media.
I know their used to be EQ's that had extra inputs. Not for sure what is on the market today, but I would think you could find something that would give you an input to your system.