I am running an iPhone 4S through a Griffin TuneFlex 9865. After just discovering the line out jack I have helped uncovered another problem. Now, while then engine is on there is a high frequency buzz aka alternator whine, that varies pitch based on the engine RPM. Are there anyways to stop the high frequency noise, or at least reduce it. I think my volume level is quite low from the line out, and is requiring me to turn the radio volume up much louder near maximum, which might be revealing the issue. How can I fix this? Do I need an amplifier?
You're discovering the joys of noisy electrical grids in cars.
Nope. You need a filter.
And filtering noisy car electricity is...tricky. You can't just create new, separate paths to ground because there aren't a lot of choices for where ground is in a car.
You can try putting a simple choke filter on the line between your player and the input to the stereo. That's the cheapest and easiest way to try and fix the problem. Something like this is sufficient.
If that doesn't cut the noisy you need to filter the power. Finding one of those car DC to AC inverters with a built-in USB port is likely your best bet. Something like this is what I'd suggest you try if the choke doesn't help.
Chasing down electrical interference like this is the bane of car audio installers and all-too-often is an exercise in futility. The line level cable coming out of the TuneFlex is unbalanced and prone to such interference. This situation is made worse by the close proximity of the 12VDC accessory plug and the audio output circuit. (The 12VDC power outlet on most cars isn't particularly clean and is often a seemingly direct pipeline for alternator whine.)
Things you can try:
Clean the dock connecter, audio jack, and audio cable ends with rubbing alcohol or a suitable electronics cleaner.
If you have the skill, check to make sure that the power connection to the back of the lighter plug is solid and "clean". There are various noise chokes and filters that you can try too, but the specifics of choosing and installing them is a science onto itself.
Reroute the audio cable. Sometimes a slight change in path will make a big difference in interference noise.
Change audio cables, and switch to the shortest cable you can use when doing so. Try to go for a quality cable. You don't have to go completely overboard with this but some of the cables that ship with devices, or the type that retract on a spool, are of a lessor quality.
This may help, but I don't hold high hopes. The proximity of the audio out jack to what is apparently a dirty power source is going to be difficult to overcome. Good luck.