Hi Matt,
Your amp is definitely the cause of the problem.
I've looked into this myself and there' a few different opinions depending on what you may have researched online.
Don't believe everything ebay sellers tell you about amps being interchangeable and compatible, especially one with a lady's name based in Ireland - who also convinced me to pay for an amp and pay with paypal as a non-business payment, only to fleece me by not sending the amp to me. I won't mention the name on this forum in case he's a member of the forum.
From personal experience, many Mazdas with Bose amp setups (including my 2nd Gen GH 6 Sport luxury model) have specific coding in place so you cannot just take an amp from a Mazda 3 with the same three physical connectors and plug it in and expect it to work. It's annoying and no one linked to Mazda has given me a half decent explanation why.
I can only assume Bose amps can be configured (with the correct input codes/programming) to perform differently, e,g. to recognise different speaker arrangements, where the number of speakers may vary from model to model.
I've tried borrowing an amp from a 3rd gen Mazda 3 and 6 with the same connectors into my car but the volume is almost inaudible even when my volume is set to the max. The info I got frm a repair company in Surrey and another in Scotland led me to believe this was purely down to how these amp are coded.
I've also taken similar looking amps from a Mazda 3 and checked what's on the PCB, and after I googled the components they are physically identical - so unless I've missed something, this leads me to believe the coding issue is at the heart of the matter.
IMO, the best approach is to get your amp fixed. You'll have seen a company on eBay advertising a repair service. I've spoken with them and they keep their cards close to their chest about what they do to fix the amp, but unless you know the exact part to source and you're great at soldering, there aren't may other options.
I think the transformer (big yellow squared component with a wire coil in the middle) is the cause of my problem, as I know it's not the capacitors. However, I cannot source a 100% working second hand transformer and I can't source a replacement part
I wouldn't buy a used amp from ebay, for £70+ as it's not cost effective considering it won't have a warranty. These bose amps are fragile so they will break eventually and unless its been refurbished and the warranty is transferable, it will be cheaper to send it away for repair.