Unfortunately, the AP computer is about 2 feet below the radio, in the middle of the boat, and the drive unit is in the stern, right next to the tuner. So I had to run the cables parallel. I separated them by about 4 feet, with the AP motor cable running in the aluminum pipe that holds up the quarterberth. I'm thinking of bonding the pipe to a keelbolt to help it shield the wire inside.
You should draw a diagram of the ground path for your radio and tuner. Show the battery, keel connection, hull foils, and engine connection (if any). You want to make sure that RF grounds return through the tuner ground post to the radio and that those RF grounds are not shared with anything else, especially the AP. You also want to make sure that the radio power and ground do not share a path to the battery with any instruments or AP as well. Ferrites are great but if your sharing ground or power paths noise will be induced in the power wires and once a differential signal is induced the ferrites will not choke it out (if connected in the normal common mode fashion).
Ok, so maybe that sounds like jibberish ? The system should look like the following: Red and black power for the radio should go to the battery directly and it won't hurt to put a ferrite at each end, like the ones clamped on power cords. You can add a breaker of course, or fuse, but I highly recommend not going into the fuse panel to make connections for the radio because you have no control of what else connects to the grounds/power posts in the fuse panel. THis assures no other instruments share the power leads, and if they did they could induce noise in the rcvr. Next,the tuner ground post should be led to your RF ground system, ie Keel, engine block, prop shaft(if applicable), and foil grounds. No other ground should connect their (engine block has the alternator connected their, but leave alone). The coax from the radio to tuner should have nothing touching the conductor, ex: don't let some stray wire touch/connect to the connectors at either end. The radio ground post should not be connected to any instruments or other boat electrical systems. Now make sure GPS/AP/WIND/Sounder wires are kept away from the coax that runs to the radio from the tuner. Put a ferrite at each end of the coax run, just to quench antenna return currents from using the coax as a ground return, alternately you can coil any extra coax up into a coil about the size of a fist with all turns going in the same direction and tape it tightly in a few spots to keep it together, this has the same choke effect as the ferrites.
Lastly, if you have things set up as above and you still have noise, you may have to do some testing. For example, noise induced in your wiring system will be present with or without the antenna attached. Test for noise without the antenna, if it is present you likely have a wiring problem. It the noise is only present with the antenna present, and tuned, then your other electronics are likely inducing noise via the antenna. There is a small chance of noise coupling from a unit, like the AP computer, directly into the radio and distance is a big help.
Hopefully these comments are of some use. If you want any additional help let me know.
Regards,
Brian S/V redsky