I just did this in my Sprinter. (Assuming ZE alt = GE alt)
Basically your current alternator has a bunch of wires out. The fat white one (or maybe two of them) on the spike is the 12V generated. The rest go to your voltage regulator on the strut tower.
The voltage regulator will also have 3 other wires coming out of it. These wires need to be reconnected to the internal regulator of your new alternator. They "should" be the same colours coming out of the ae86 regulator and on the 4AGE alt plug. Once you've reconnected all these wires you'll realise that you have nothing plugged into the regulator so you can turf it.
The external regulator also has a fat white 12V feed, this can be removed too.
It was a bit of a hassle to get my head around, but wasn't hard to do once I got it worked out. If you need more help I could scan an ae86 wiring diagram for you, but it would take a while.