So if I buy a junkyard ECM I will still have to pay the dealer to program it? Should I have the dealer T/S to make sure that the ECU is actually the problem before I spend the money on one?

 

If the junkyard ECU is cheap, here's a work-around to check if the ECU fixes your problem.

Get a key from the donor-car where the ECU comes from. Duct-tape the 2 keys together so the handle part of the keys are right against each other. Now the immobilizer will pick up the key that "belongs to" that ECU (along with your present key).