Presumably, you have no manifolds now on your head?
If that is the case, see if the new intake lines-up/bolts-up properly on your head (with no exhaust manifolds/headers in place).
What exhaust manifolds/headers are you using? Do they mount up properly to the head (with no intake in place)?
If the intake and exhaust manifolds mount up OK, then you will have do whatever grinding needs to be done. Be careful.