if its a shell build i wouldnt be leaving the old wiring loom for the old ecu in there, get the loom open and get rid of it, it will always look untidy. if you leave the other ecu in place, where will you mount the new one?

i would rip it all out and fit a decent alarm while your there.

the only two feeds you will need from ther old loom are the oil pressure gauge and light iirc, and you can make a simple sub loom up to feed these directly to the gauges.