Engine noise almost always comes from the ground wire(s). I had a similar issue with my car stereo. I had 2 newer alpine amps and 1 older phosgate amp. The phosgate amp had engine noise and the other 2 didn't. They were all grounded in the same place. If the amp sees too much resistance to ground you can get noise. I think the circuitry in my alpine amps is better and they are more resistant to noise. Your alpine hu was probably just a better piece of electronics than your new hu. You may need a better ground to get the noise out of this hu. I ended up moving my sub amp ground to a different spot and ground off all of the paint. I ran better ground wires (I was trying to use speaker wire) and removed the paint from the original grounding point. Mine went away almost completely, I can live with it because I can't hear it unless I have my ear by the speaker. The longer ground wires are and the thinner the gage the more resistance and possibility of noise.The noise you have is alternator whine. It is very annoying. I would try regrounding all of the items at your head unit that have grounds. I don't think the factory ground wire is considered to be a great ground. Your grounding point should have no paint or rust and would be best the bolt through the ring terminal(s) went directly to the frame. You may need to try grounding it different places and ways such as 2 different points for the 2 devices. Unfortunately, this is the single biggest pain in the *** problem you can get with aftermarket components. Here are 2 links that will help you better understand what you are dealing with:
http://www.termpro.com/articles/noise.h ... 999502.pdf
I say this with all sincerity...GOOD LUCK!