Ya know what's most difficult about this one is that we know practically everything on that engine is NEW !!!

Did you ever run that ground braid from the valve cover to the back of the head ????? Just curious...

On to your problem at hand.

Yer absolutely certain that you've got the vacuum lines plumbed right ??? Particularly on the EGR circuit ???

What's the manifold vacuum doing during the period from cold start to warm-up to "closed loop" ?

It's pretty easy to swap the EGR circuit and the CANISTER PURGE circuit when re-plumbing vacuum lines. Make sure you didn't do that.

There are two vacuum ports on the bottom of the throttle body, are you certain that the one toward the rear of the engine is running down to the blue vacuum switch, then up to the backpressure transducer ? And, the other is going down to the TEE that splits and feeds vacuum to the VSV's on the inner fender ?

Did you re-check the ignition timing ?

What do the plugs look like ? Probably not been runnin' long enough to tell much from them though...

I'm just pluggin' for ideas here...