If you're absolutely intent on doing it that way, then you'd probably have the passenger side H/E as the last in the chain as it'll be the furthest away from any hotbits.
To be honest though, even though you're pretty much decided, I still can't figure out why you're making it harder for yourself. Your proposed setup would be more complex (ie failure prone), expensive (extra mounting cost, extra H/E), take up more room, involve cutting, make the core difficult to locate/mount & by no means outperform a front mounted H/E & core mounted in engine bar (passenger side barrel).
Don't get me wrong, not trying to discourage you, just my 2c & giving you my perspective. Final point, if I were in your shoes & mounting the core in the boot, I'd be using some a LOT better than a PWR barrel. Something of similar size to this (wayy too big to fit that core in the engine bay):
http://www.hitman.hm/hussler.htm