What intake do you have? The gt500's dont work with the Boss intake without extensions. I never tried my in the stock intake but i assume they are to short for it as well.
I can't add a lot to this thread other than to say that I believe you have to confirm that both the connector as well as the length are the same. I've seen some spacers that fix the length issue, but am unsure on which connector is correct. My .01.