Let me recommend that you do away with the Mach460. Maybe you can find a buyer on ebay... someone to whom restoration is more important that quality sound.
A nice 4 channel amp in the trunk, polk components in the doors is a first step. I would just make a clean install by pulling the mach cables and selling them with the mach speakers and amp.
The boom box presents an interesting choice: You can pull the speakers and replace them with aftermarket speakers. I'm not sure what size aftermarket speakers fit in the boom box. I did this in a vert, which has different rear speakers than the coupe. It worked great though.
Simply hanging speakers on the rear shelf won't sound good.
Or you can remove the boom box and get some smaller enclosures to house your rear speakers. It might not sound as good as the mach's enclosure, but it will leave you with more room in the trunk... room for subs.
I have a 6" sub and it hits hard... you can go 12", but I'm not sure how much of an enclosure will fit. I'd rather spend $ on a quality 6" sub than a less expensive 12" sub (for example: 6" JL might sound better than a 12" brand X from Wallmart).
Finally, the stock power line in the trunk. I pray that the fuse protects me, but I have been powering a 500W JL monoamp and a 4x60W amp from a single 12V wire that went to the mach's boom box. I have a 1f cap there. Works fine so far.