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Well, having been through this several times, I've found once I wired the thing I didn't have to rewire unless I changed EEC's to a different unit. So sticking the new one in the official mounting location wasn't a big deal to me.
Also, the back is in fact exposed inside, so if you need to have a J3 adapter and wire hanging off, you can route it tightly behind the EEC and up over the shell inside and tie that under the dash.
I dunno, all of the changes I made once installed, pretty much were code/data changes, until I switched back to the original.
Well, I just dug through my old parts and found two complete car harnesses, one Cougar and one Mustang(BINGO!!!). So I'll probably just end up putting it inside and relocate with the longer harness.
I relocated mine so it would be easier for me to make program/tunning changes when I was on the road or at the track. The mass air conversion harness had enough length to allow the ECU to be relocated.