Ahh right - not having (or being able to find) a wiring schematic showing the routing to all the speakers I wasn't sure, I thought the sail panel subs were the only ones driven by the slave, didn't realise the trunk speakers were as well.
No, the head unit is fine in another vehicle, and the front/rear fade function works correctly. Also, the trunk speakers work fine it's just the sails not giving any music signal; the door mids work as well.
And the slave amp is not above the wheel well, because it's a 94 it's down by the rear seats and a ***** to get to.
Ho-hum, looks like I have a fun weekend ahead wiretracing!