On the 2001 engine, behind the sprockets box, there is only one blue wire that comes out and gets connected to the connector near the battery.
On the 2004 engine, there is a red and green wire as well.
I did an engine swap from 2001 to 2004. What do I do with these extra red and green wires?

Those are gear position sensors for the newer ICU.
You can ignore them.

Thank you!!
I am having some new problems now. Do you mind giving some insights into what could possibly be wrong? I have created a new post for it..