Sounds like they've been disconnected. First check rear of headunit. If plugged in there and still not working I'll tell you about the other plug to check.

Right, next place to check is behind the pannel at the end of the dash that contains the airbag switch (with the key slot to turn the passenger one on and off). Open the glove box and from memory it's 2 screws to get that panel off. Then under that panel there is a White plug secured onto the end of the dash. This has to be unplugged if the glove box is removed and can be forgotten to be replaced together and for some reason this plug controls all the speakers.

Jon.

Remove lower glove box and pull carpet back and there is a big black washer in the bulkhead, this is where I've run cabling through and where most people do.

would suggest the fuses, but if stereo works there must be something done with the wiring, althou i cant get my head around why would you have speakers in parcel shelf if they're not powered by an amp... are none of the speakers working at all? you can check the parcel shelf ones with your home cinema, just plug them in instead of any other speaker, obviously volume to 0 and then go up to see whether anything comes out of it...