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.