The LT5 motor I am using has 96 wires coming from it to make it run correctly, (16 nozzles, that's 32 wires alone!). I went to a Pull-A-Part wrecking yard and found a large wire conduit from the driver's door of a large car (A Mercury I believe) that the wires for the windows, speakers, door locks, etc go through. I used a hole saw and mounted it low on the firewall above the transmission. It can't be seen. Just remember to feed the wires through it as you install the motor or you will never get them into the opening.
I'm going with the Mil-spec connectors. 2, side by side. I think one is around 40 pin and the other is around 60 pin. They twist and lock together. Not cheap but very nice and solid connection with no worries.
Problem with the AAW bulkhead is there is no 10 / 12 gauge pins. Mil spec is nice, but we do a lot of them exactly like Steve said, trans tunnel at firewall trans tunnel union
I used a MegaSquirt fuel injection controller for my Camaro. I ran the wires through the bulkhead that all the other wires run through. I bought a Painless wiring harness (before I knew about AAW, will probably try them on the current project) which had just enough open spots in the bulkhead to connect in the fuel injection wiring. Worked out good for me, but wouldn't have if the fuel injection setup would have been sequential instead of batch. Another option that I have thought about would be to get another bulkhead out of a late model car and cut the hole for it. Wouldn't need the fuse box part of it, but would be a some what clean install having it look "factory".