look here for the wire hookups
http://ipdb.org/showpic.pl?id=857&picno=50056&zoom=1
The 2 thick yellow and yellow/white wires should go to the 2 pin connector on the stock board. On yours these appear to attached to the trailer plug with the black and red wires.
There are 8 wires that go to the pf and backbox lamps (and coin door lamps) (these are attached to the other side of the trailer plug in your machine). These are 4 solid colors and 4 white with a colored stripe (colors are yellow, green, purple, orange/brown). These are normally connected at the 9 pin molex. 4 solid colors on one side and the white ones on the other with a blank pin in the middle, doesn't matter which wires are on the left or which are on the right.
Normally there should be a 3 pin connector with 2 wires that is for the GI relay (the aftermarket board has a 5 pin connnector here), but the 2 empty wires are not the correct color (should be red and black with a stripe). Are those 2 loose wires possibly some of the 8 GI wire. Will have to check the schematic to see where you say they originate from.
Flippers should be active during the test mode, they don't have a coil number in test. They are turned on by a relay and that relay is always active during the test mode. The flippers should always have voltage, the relay supplies them with the ground path.