It could be the line level feed, but from your excellent description, I am now even more certain that the fault is earth related.
Just because another head unit works does not prove anything, unless its the same make and model as all have their own tolerances - The NCDC range were never meant to be used with aftermarket amps, but that does not mean that you can`t use them, just means that you have to be a little more carefull in the installation.
The noise is power supply generated and not from the ignition or fuel pump circuits which can be confirmed from the information you have replied with. Although this noise is generated from the alternator, the alternator does not require suppressing. the noise is occurring due to an "earth differential" either on the line input, or more usually on the main earth to the amplifier. Starts to get technical after that - so I`ll shut up on that bit now.
OK, non technical instructions.
Where and how is the amp fitted and mounted?
On the input side of the amp will be an adaptor (matchbox size) with cables going in and RCA/phono leads coming out. This wil either be situated in view near the amp, or may be mounted at the rear of the head unit with longer RCA cables fitted. let me know what you can find.
On the amp is a -ve terminal, should have a hefty thick black(?) cable to it - follow this cable back, which should only be a maximum of 18-24 inches long and let me know where and how it terminates. It will probably be a cable attatched to a bolt in the floor, a panel or around an existing bolt - it wont physically attatch to any other wiring. it may or may not have a large crimp with a ring terminal on it.
Let me know what you can find, and I will try to suggest something.