[eakes]

Alternator whine is a nasty animal. It can be picked up due to a ground loop on the DC for HU and amp, radiated into the audio cable between HU and amp or get into the amp because of improper DC filtering in the amp or HU.
Probably the most common is ground loop. To help solve this both HU and amp need to be connected to a good ground. The Titan dash wiring connects the HU to ground which turns out to be at a different potential than the amp, therefore the first step is to insure a good ground at both HU and amp. The amp should be grounded to the chassis in an area where any paint or corrosion has been removed from the chassis metal. Likewise the HU needs a dedicated wire from its case to truck chassis, again the chassis attachment area needs to be free of paint. You can also try connecting the HU case to the ground terminal on the amp. Use at least a #12 wire for this connection. The amp ground wire needs to be the same guage as the wire used to feed its power.
The audio lines between HU and amp need to be good quality and separated from any DC power cables by at least 12 inches, preferably run the amp DC and the audio lines down different sides of the cabin.
Set the audio gain on the amp as low as possible.
If you are using an LOC and are connecting its ground connection, it should be connected to the HU case ground wire.