OK if U are coming straight out thru inner and outer guard using 90 degree bend, straight piece 4"SS then a 90 deg silicon back (exterrnal) toward pillar A this is fine. Worry about the hole thru guard after you are happy with good placement of box (of course watch how alignment is going).

For the silicon from box toward turbo it can have leg trimmed to appropriate length. U can afford to move box towards firewall and closer to eng to drop height and give more room to get 90 deg bend thru inner guard. If leg length of 90 degree silicon to join up to turbo is short U can just add a short length of SS 4" tube and a straight silicon to turbo inlet.

You can alway put new holes in to secure LS1 to body panel.