Clearly, the Megasquirt ECM needs to be mounted in the passenger compartment as it is NOT designed for the under-hood environment. Though since EVERY poster above has made various suggestions of mounting the box somewhere in the passenger compartment this might be a bit obvious.
I like the idea of using bulkhead connectors between the engine compartment and firewall, they are a bit pricey but I think they would facilitate wiring and future engine removal.