Since I won't be using the egr spacer do I plug the coolant lines that went to it?
yep
You can get away with using those rubber vacuum caps to block the coolant flow however I suggest replacing them every once in a while and securing them with a zip tie.
Whatever you do just secure those fittings well so they don't leak or your cap/cover whatever, doesn't blow off. It's happend to me and it ain't pretty.
Just plug them together with a nipple of sorts and little hose clamps.
Thanks for the answers,up and running.
Quick question.
You said you arn't using the EGR spacer. How did you secure the linkage bracket to the intake?
Bolts directly to the intake on the Cobra... BTW the EGR spacer is also part of the intake, but does not have provisons for the coolant lines...