There will be a few plugs not used which are below the battery, this was the wiring for the auto control. The only two that are used are the one at the top, which you just put a jumper in (two pin plug) which is the starter inhibit. and the grey one below it which you use three pins, one for supply to your neutral and reverse switches and the return from your tranny switches, If you need some pics, should be able to help out.
If you added the loom from the manual to the existing wiring, it will have all the plugs for oil pressure, knock sensors etc, which might explain the left over plugs.