I don't know at what part to respond to. I'll start at this, why in hell did you swap the engine out? It's no 16 valve and will never be a 16 valve, or a 2.6 six cyl. Why, was it bad, or are you looking for more power???? Clue us all in.
I think the thing you need to do is go find a shop that is going to work with you. Because trust me, you are going to need a shop that will work with you. The reference sensor is just a fancy enclosed magnet. It picks us the signal from the flywheel, that made from metal