I've done this on mine and once all the trim is off it's not too hard to work out what wire does what. We did do it in a bit of a rush though so the connections could be improved as we cut the cars loom and then cut the ph2 loom out of the boot. One day i'll go through and shrink wrap them properly. If you had all the time in the world you could feed the original loom into the new boot properly.
As for the extra wire, i think it was something to do with the locking mech. The phase 1 has a key lock, but the ph2 doesn't.