Just my personal take, but I'm always hesitant to put critical wires in areas where they may be subject to impact. Under the carpet they're shielded, but overtime they'll still experience wear and tear, especially if they're spread out. My plan is to locate it either behind the dash somewhere, or to build a center console and locate the ECM inside of that in front of where a floor-shifter would go.
I would also avoid putting them on the underside of the cab, mainly because anything that COULD come in contact there (which would be unlikely) would be doing so at speed.
I plan on using bulkhead connectors to go from the cab to the engine bay. Will require more planning in wiring, but should make for a cleaner install in the end.
http://www.summitracing.com/parts/aww-500666