Not to say anything bad about your pro since I don't know his work, but some of the installs I've seen that was performed by professionals looks like they were professional paper hangers, not professional stereo installers. Being a pro doesn't necessarily mean the guy does good work so I'd not take the guy's word as gospel. You might even take it by another shop for a second opinion.
Now, for my suggestions which are not based on me being a stereo install pro, but based on me being a telecom tech who has seen some weird sources of electrical interference in his career:
Where exactly is the wiring running from for the new parts? If it's run alongside the trans tunnel then moving it away from the trans tunnel might help. You want to be at least a foot away from possible interference points.
Was the power wire twisted around the ground? If not, doing this can help as twisting the wire will cancel out interference. You're looking for a pretty tight twist, like 2-3 twists per inch on a 14ga wire. You can also install a grounded shield on the wiring, grounding both ends of the shield on the power lines and grounding one side of the signal wire, at the amp.
Was the power line run separate from any speaker wires or were they run alongside each other? They should be at least a foot apart, and when they come together at the amp they need to come in at the amp at a 90 degree angle to each other for as long as possible.
Have you checked to see if all vehicle grounding points are good? A corroded body to frame, frame to engine or body to engine ground point can cause radio noise.
Where was power taken from on the entire system? Was any of it taken from a wire that shares the fuse that was pulled? If so, moving to a power wire from a different fuse may help. I know main amp power won't come from there, but if the radio is getting any power feed from a wire that shares that fuse it might be bleeding over.
Where is the amp and the stereo grounded? Disconnecting the ground from wherever it is and running a separate ground wire from the amp and the stereo directly to the battery may help.
Any unterminated wire can act as an antenna. That's essentially what an antenna is. Any loose, unused wires need to be terminated, or removed as close to the connector as possible (leaving enough to splice on a new wire if necessary) to eliminate it from acting as an antenna. This is directed at any wiring adapters as they are designed to accommodate as many different stereos and vehicles as they can. These adapters may be connecting to the stereo on one side but nothing on the other, effectively turning that wire into an antenna which can then receive interference and bleed it into the stereo signal.
Hope some of this helps.
