Marc, the key is planning. Make a drawing of the engine compartment from the top, and mark where you are going to have all the EFI goodies that you will need. This will include the air temp sensor, water temp sensor, throttle position sensor, MAP sensor, IAC if you use one, crank and cam sensors (or distributor), injectors, and coil(s). Where you mount this stuff will determine how much of the EFI wiring you can hide. As far as the wiring itself, the universal harnesses that come with the MS3-Pro have 8 feet of untrimmed wires, so you mount the EFI box, hook up the cables, then feed them one by one through a hole or holes through the firewall, to their destination, along the route that you have drawn up in your drawing. Leave some extra wire on each connection, so that you can bundle them together in cables when you are done, then wrap them with a protective wrap like that Painless Wiring Powerbraid stuff. When you are finished you will have a few black cables running from the key components in the engine, back through the firewall to the EFI box. Here's a picture of the plan I made for my Shelby clone:
On my setup I went through the firewall in three discrete places, to hide as much of the wiring as I could. The top and bottom cables in the picture are basically invisible, hidden behind the fenderwells or the roll cage. You do see the cables going to the injectors, and also the cable going to the TPS and the ATS. Also, I mounted the two MAP sensors on the firewall, but they could have easily gone behind the firewall to hide the wiring. FYI the second MAP sensor is to monitor crankcase vacuum. Since this is my SOHC I also used two cam sensors, one on each cam. The cam and crank sensor wiring goes out of the engine bay on the driver's side, then up the roll cage bars and back into the firewall. Same with the oil temp, oil pressure, and fuel pressure sensors. Those are all there so that I can log those parameters with the EFI system, while driving down the road.
Hope that helps you get the picture. FYI I'm hoping to have an update on my dyno mule this weekend, with all the EFI ignition stuff installed. There will be more information in that post - Jay