You should have been able to use pin 1 on the 10 pin like it was and pull pin 10 on the 10 pin. On the 4 pin, leave the IR wire where it is on the motherboard and put a jumper in pin 3 from the cruise m to the motherboard. You can use the harness as err sent and move the IR wire to pin 3 on the motherboard too. Either way, you need a wire in either 1 and 1 from the motherboard to the cruise m or in 3 and 3 in addition to 2 and 4. You will end up with 3 wires from the cruise m to the motherboard. Put the IR in pin 1 or 3.
For the time being, just use the harness that came with it. You will lose your IR until you plug it back into the open hole on the included harness.