While that does help for now, if you actually have yellow to red and red to yellow at some point, this will throw off the readings of a thermocouple in small ways. The wires are different metals and connecting them like that causes errors.
Sounds like somehow your red/yellow is switched at the EMS connector. For the best accuracy, you should really fix it up there, and then keep the red and yellow straight all the way to the EMS. If you did get a miswired harness, we're very sorry.