I've personally done a tuck in my EK, and I did everything properly. Now every time I want to add a wire for something new, I have to take the fender off or find a way to get power from the harness which is now mostly under the intake manifold.
To make a long story short, I bought a fresh (used) harness off of ebay. I'll be installing it with my VTEC conversion, and putting the battery back in the stock location.