You will need to get under the front end for a couple of connections, so you may want to drive it up on some ramps or put it up on jack stands to start off (I did the latter; shouldn't make any difference). Mine is a 95 wagon, and I believe there are some differences so sorry if I inadvertantly misguide you on something. I had to completely remove the plastic air inlet that ran over the top of the motor from the airbox to expose all of the harness (one of the wire harness connections was on this thing, too. Had to put that connection on last). Also removed the plastic cover from the top of the engine, in front of the engine oil filler port. The majority of the harness runs along the top of the engine. On my car, there is a clearly-visible plate on the very top of the engine which is held in place by six hex-head bolts which, when removed, exposes the ignition coils (I think they're the coils. Somebody please correct me if I'm wrong). Some of the connections go under the plate.
I started at the battery end. Fattest part of the harness with the largest connector socket for the computer. I removed the battery from the car, then pulled the computer connection and popped the new wire in. Did this the whole way. Go slowly and remove/replace one connection at a time, or where this is not possible, as few disconnections/reconnections as possible. After making connection at the computer and laying the wire around the back of the battery tray, you have to then go through the firewall into the engine compartment. It runs up at the very top of the firewall in a small rectangular notch cut out of the firewall, and is held in place by some plastic. The plastic trim that holds the harness in the firewall notch can be moved and you can just lay the harness into the notch and then pop the plastic bac over the top. Just look at it for a few minutes and you'll figure it out.
Then you head right for the rear of the top of the engine. At the top of the motor, sometimes several connections will need to be removed before you can plug a new one in. Just go slow and pay attention. Jot down some notes if you need to.
I found that two of the connections required some contortionist skills from underneath the car to get to. One of them you come across almost immediately. A single wire heads down along the side of the motor at the very beginning of the long rubber molded piece that screws down to the top of the engine. It's hard to do disconnections/connections on stuff that you absolutely cannot see. This was the hardest part of the job. You have to first find the connection by feel from below (a friend guiding you from above is helpful to tell you which way to go), then you need to just feel it for about 5 minutes to figure out its orientation. Look at the connector on the new harness and figure out which way you would have to pinch the old one to disconnect it. And remember that orientation (by feel) so you can just pop the new one on. Most of these connections are of the type that you should hear an audible "click" signaling a positive connection. The other contortionist connection was at the other end of the long rubber piece. This was the worst one for me. The wire heads under the intake manifold.
I needed two (or was it three?) black zip ties (5 inch) later on. A couple of the originals had to be cut, but there are a couple more zip ties (larger ones) on the car that can be reused if you're careful in removing them. The last connections that I made were at the very front of the motor where the plastic cover goes. Two of the connectors are nearly identical (one bends 90 degrees but otherwise has the same pin configuration as the straight one). I forgot which was which and guessed (correctly!). Watch out for that.
Put all of the stuff back on at the end and reconnect the battery. Then pray to God, with the phone on speeddial to AAA for a tow. This is why I did jackstands, so I could just lower the car down and push it downhill and across the street so I could get a tow to the nearest shop after screwing this up!! Turned out to be not so bad. Just be patient and go slowly.
Total time was 3 hours or so, but spread out over 5 (contortionist connections required some break time to recoup!)
1995 E320 wagon