Those EGR holes in the intake and heads are standard for decades. You can use them or not, since fuel injection there is virtually no flow in them. Those are the first gaskets that I've seen that give you a choice.
Sand the spacer smooth along the sides for painting, and sand between coats.
For the lifters, I'd look in the block at the lifter bores. See where the oil galley holes are, face the lifter towards them. Like I mentioned before, there may be an oiling groove around the lifter at the holes.
You can use Ultra Black or Ultra gray, or the other Ultra series for gasket material. I also prefer a gasket, with spray tack often times, but the RTV is really good stuff. It can take all of the heat, fuel, oil, and pressure that gaskets see. Regards,