Thanks for taking the time to look at it and snap some photos Scott. I'm pretty sure I have it hooked up right. It must be something to do with the 04 engine and the 00 ECU.
My old intake manifold has 3 hoses coming off the back near the firewall. This new one just has 2. What's weird is the one hard line that sticks out under the intake was not use on the old engine. The end of it was all dirty and nasty where as the one next to it was clean form where the hose was connected.
I guess I'm going to have to break down and head to the dealer and see if they can figure it out.