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Definitely make it a point to closely inspect the harness along the EGR pipe.
If you should end up having to inspect the bulk of the harness, don't let it intimidate you, man. Get a Sharpie marker and a roll of masking tape. You can have the bulk of the harness disconnected and lying on top of the engine in about half an hour.
Start by disconnecting the battery completely. Might as well remove it too. This will give you more room to work.
Get under the car, start at the alternator, and work your way towards the battery. Use the tape and marker to label your connections as you remove them so you know what goes where at installation time. There is a spot where the lower rear harness is clipped to one of the intake manifold support brackets. You can cut the clip entirely and just zip tie the harness back when you're done. Once you've disconnected everything on the backside, down there, you can go topside and pull that section of the harness through from where the battery sits and lay it up and out of the way.
Next, start by disconnecting the O2 sensor. I believe this is the end of that section of the harness. Begin disconnecting things there and work your way back up to the radiator cap and over the valve cover (next to the timing belt). You will then disconnect the coil pack, MAP sensor, IAT, TPS, and IAC connections. This is the bulk of that leg of the harness.
Finally, disconnect the EGR solenoid and CMP, working your way, again, back towards the battery area. You will need a socket to remove a clamp that holds the harness in place there (even the factory knows you want to keep things from touching that pipe).
At this point, you will have access to pretty much all of the harness, aside from that section that connects all of those to the fuse panel and ECU. If you're lucky, the cause of the short will stick out like a sore thumb and you'll be able to attack the problem head-on, standing up, with decent lighting so you don't fuck anything up.
I hope you don't have to go this far, but the point is to illustrate that harness removal and installation is one of the easiest parts of preparing to remove the engine and, so long as you label your connectors, you'll make quick and easy work of it. Just start at one end and begin unplugging/labeling things and you'll be fine. It's no different from hooking up your xBox.
Good luck to you.
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