I just finished pulling the harness from a 94 Legacy on Monday so it is fresh in my mind (this was about the tenth I have pulled in the past 18 months).
My routine is:

1. Remove front left fender - just a few bolts and off it comes.
2. Remove and save the black fuse box in the engine bay - including the battery cable. The box has a number of plugs that you disconnect and there is a group of relays that come out as a complete assembly. Very useful box for future use.
3. With the dash out of the way split the large gray and white connectors by the steering column (when on the left). This makes it much easier to get out and handle afterwards.
4. Also remove fuse box on left side and un plug all the connectors. I save this box and mounting hardware (mount it behind the clove box in the Vanagon for head light relays, additional fuse etc.).
5. un plug all connectors going to the ECU and dash.
6. cut wires (but keep connectors for future use) of all wires that are clearly lights and other accessory type wires.
7. pull on the harness on the left side and the grommet should just pop out - this will allow you to feed all of the left side harness out through the hole where the grommet was. You will also be able to feed the wires and connectors from the engine bay out through a plastic grommet in the fender well. This should liberate 1/2 of the harness.
8. now take the nuts off the heater fan assembly, A/C evaporator and heater core ( be sure A/C and heater hoses are removed in the engine bay). You should be able to just pull the fan assembly out easily, next comes the A/C evaporator and finally the heater core (some times take a bit of fiddling around to get the heater core assembly out).
9. with these out of the way - push the centre engine bay grommet back into the passenger compartment and slowly poke all the connectors and loom through the fire wall into the passenger compartment ( start by pushing the smallest connectors and wires first).
10. now you just have to disconnect the harness in the passenger compartment - including the ignition and fuel pump relay bracket
11. The harness should be ready to remove.
12. I always pull the harness out of the dash as it is a good source of colour coded wire - for future use.

I hope this helps - as you can see I end up with lots of stuff for future use - then throw it away when I can't find any place to put more stuff for future use?????,

Tom
Burlington Ontario
http://www.subaruvanagon.com/

Thanks to Tom Shiels from Burlington Ontario