Oil in my intercooler and tubing

I just recently installed my used D1SC on my 99 Cobra. I have a blow-thru MAF so my bypass valve is vented to the atmosphere. I noticed after a few days that I had some oil on the top of the tube going to the throttle body, oil on the top of the coolant crossover tubes, etc. I pulled the tube between the head unit and intercooler loose and let it hang down and oil started running out of it. Does this mean a seal inside the head unit is bad?

Depends on how you have your PCV system hooked up. If it's hooked up per ATI's instructions, you're probably drawing oil from the PCV system and it's collecting in your tubes.

I removed the PCV and put breathers on the valve covers before ever firing up the car.

In that case, it sounds like you may have an impeller seal leaking.