common guys this is the forced induction area, thats a Greddy turbo manifold.
ok now about the manifold, i would NOT cut down the center section, its concept is similar to the twin scroll idea which is to say it helps boost come on sooner. From what it looks like that crack is only internal and should not cause any kind of boost leak or any leak for that matter. I would just put it on as is and go with it
Now i do know you are in the process of building a shortblock, i have said it before that Greddy kit is a bit small for what you have in mind. If you can sell it locally for a $1000, save up another $1500 and you can buy a nice AFI kit which is capable of much more power. But if you are happy with what the Greddy kit has to offer just put it on and rock and roll.
also it may be worth a shot to call greddy to see if they will cover it under warrenty?