I have also the same problem with my car. if you shut the car off it will stop so that leads you to believe it is ignition or the alternator. My car is getting the noise from the alterantor. if you disconnect the plug in connector on the back of the alternator and start the car you will find, in most cases the noise goes away.
I gor the problem when I hooked up my amp also. The first setup was my kenwood deck and the amp, I was able to disconnect the ground side of the rca inputs to the amp and that cleared up the problem. Now I have a fosgate power 300 amp also and I have not been able to get the noise to go away. I was able to minimize the noise with a high current schotty diode from the main power to the battery, but not totally get rid of the noise. You will just have to play around with it to find what works for your system.
On another note, you described what made the noise go away by disconnecting the fuse link (the black link I believe) that indicates you have the amps hooked to the battery terminal. The problem with this connection on the car is that under high current loads you will burn up your connectors for the black fuse link over time, as all of the current the amps are drawing is going through the link from the alternator. I did this with my fuse links and got to looking at the schematic of how the car is wired and found the alternator wire(white wire) was connected through the black fuse link and when I was taxing the system for current to run the amps I was drawing to much current for the link, and the wire got hard, and the connectors, spade lugs, burned up over time.
What you will need to do is to run at least a #6 wire from the alternator to the starter plus wire to the battery, that way you will provide the battery with the extra current it needs from the alternator directly to the battery and bypass the black fuse link, and the rest of the car will continue to operate through the fuse links like Nissan designed them to do.
Let me know if you find a solution forthe noise. I have installed filters on the power to the amps, filters on the line level inputs to the fosgate and neither of those parts have corrected the noise problem. I have not tried the big 1 farad filter on the power cables, but I dont think that will help anyway. The line level inputs are the key to the noise problem, so if you try something work in the line level input area to fix the problem. You need to somehow isolate the grounds of the line input to the amp and that will fix the problem, but so far all the crap that you can buy doesn't seem to work and is a waste of money, at least it was for me, but you never know, different designers configure the front end of their amps differently and you just may get lucky with your setup.