Since I haven't been following any threads describing your build, I'm not clear on of what your system consists - or what your last suggestion actually means 
I hear a lot of talk about ground loop "filters". No such thing. There are ground loop isolators and they can do a decent job, and many amps have a good degree of isolation onboard. (It should be noted that most autosound ground-loop isolators have souch a lousy frequency response that if you hooked one up to an RTA, you would throw it in the river.)
An iPod on a charger in a car often is a noise source. Usually that is a ground loop - but it can also be a charger without power filtering! Cig lighter sockets are famous for having LOUSY grounds, btw.
So I don't know if our iPod is the preamp (driving the amp directly) or is connected to a HU or what, but I would improve the cig lighter ground first, and I MIGHT put a powerline filter in series with the cig lighter power wire (nned a high-amperage one if it ever gets used for a real lighter : )
If the iPod is the preamp, how high is the JL gain? Remember, all systems have noise, it's just inaudible in the good systems
If the iPod is connected to the HU, I guess I would take the cig lighter ground and re-route it to the HU ground (the HU ground in my installs would have already been run to the amp ground).
BTW, if I recall correctly, the iPod preamp out can't really drive a Jensen Iso-Link well (best ground-look isolator on the market). Markertek also has a cheaper one that tests pretty well. (Rolls?)
I hear a lot of talk about ground loop "filters". No such thing. There are ground loop isolators and they can do a decent job, and many amps have a good degree of isolation onboard. (It should be noted that most autosound ground-loop isolators have souch a lousy frequency response that if you hooked one up to an RTA, you would throw it in the river.)
An iPod on a charger in a car often is a noise source. Usually that is a ground loop - but it can also be a charger without power filtering! Cig lighter sockets are famous for having LOUSY grounds, btw.
So I don't know if our iPod is the preamp (driving the amp directly) or is connected to a HU or what, but I would improve the cig lighter ground first, and I MIGHT put a powerline filter in series with the cig lighter power wire (nned a high-amperage one if it ever gets used for a real lighter : )
If the iPod is the preamp, how high is the JL gain? Remember, all systems have noise, it's just inaudible in the good systems
If the iPod is connected to the HU, I guess I would take the cig lighter ground and re-route it to the HU ground (the HU ground in my installs would have already been run to the amp ground).
BTW, if I recall correctly, the iPod preamp out can't really drive a Jensen Iso-Link well (best ground-look isolator on the market). Markertek also has a cheaper one that tests pretty well. (Rolls?)