Ok let's reset as i am getting things muddled.

The wires from the opto under the playfield go to a joiner and then two wires go to J16 (i currently had this plugged into J2)
So if i plug it into J16 this means J2 is now blank so i need to get two wires into J2

Glad you discovered this.  This was actually my sneaky intention when I asked you to send me the partial harness.