My rear door aftermarketspeakers not working after installing new head unit on 2004 Honda pilot?

There could be several reasons why the head unit for your car does not work. The most likely issue is that the head unit is not compatible with your stereo system. You can consult your vehicle owner's manual for speaker issues.---------------------------------------------------------------------------------------
Diagnostic VAG

Put new wireing in going to both back speakers, Factory wireing is verry thin end it breaks with age. Change it over to at least 16 guage speaker wire or 12 guage, Your system will sound a lot better.

Radio Constant 12V+ Wire: Blue/Yellow
Radio Switched 12V+ Wire: Gray
Radio Ground Wire: Brown
Radio Illumination Wire: Green
Left Front Speaker Wire (+): Pink
Left Front Speaker Wire (-): Purple
Right Front Speaker Wire (+): Purple
Right Front Speaker Wire (-): Light Green
Left Rear Speaker Wire (+): Black
Left Rear Speaker Wire (-): Yellow
Right Rear Speaker Wire (+): Red
Right Rear Speaker Wire (-): White

the quickest and easiest test is to disconnect one of the rear speakers and hook a good speaker to it and see if it plays, if it does then its bad speakers and not wiring, this is the best way and easy to do, hope this helps, good day.

this vehicle will require a new cd/radio. the mother board that controls the cd/radio is burnt out

If the rear speakers worked before your new head unit was installed, then the first question is does your new head unit have the facility to feed four speakers. Some systems will only power two speakers. The Audio Shop should have rectified the fault - you paid for the installation and as the customer you have a reasonable expectation that they would do it properly and ensure that all of the existing speakers were functioning properly. It would be worth challenging them again - if they refuse you could go to Citizen's Advice Bureaux or the nearest Trading Standards Office. Alternatively, try tracing the wires back from the rear speakers to the head unit - are the wires connected up properly... at both ends (i.e., the speaker end and the head unit).

The audio shop has probably hard wired the head unit because the sockets in the back of the head unit were not compatible with the plugs that came as standard with the car. A Haynes Manual or equivalent will give the colour codes for the various wires for the audio system.

Either the balance is off on the head unit, or the the out puts (in the head unit) for the rear speakers are blown.

You need to attach the blue wire on the stereo harness to the blue and white wire on the car adapter harness. they installed a small amplifier to power the rear door speakers and unless you connect those two wires then the speakers will not work.