#1
The purple arrow is fine, it wont hurt anything. its just for the BBV
The green arrow is pointing to the threads for the coolant temp sensor. should be fine as long as there are threads there.

#2
blue circle looks fine, you could dremel it out if you really wanted to.
Black/purple: Idk, leave it alone.
Black arrow: Yes cut that out to match the outlet of the IC core.
Yellow circle: Yes cut that out to match the LIM, doesnt need to be there.
Red square: The coolant ports to the SC seemed to be blocked off, its needs to be like this seeing as the coolant cant pass through the IC core. Its good.
Red circle: I wouldnt worry about it

#3
Yellow circle: Cut it off
Blue circle: might as well cut the gasket
red line: gasket match if you want.

hope this helped. I have not installed an IC core so i didnt answer some of the things considering the PVC ect.