Intake will need a different coupler since 3.2 TB is a little bigger, or use an intake meant for the motor. Headers are interchangeable, at least the exhaust manifolds are. These mods alone don’t make enough of a difference to need a management system, just reflash the ECU and it will make any adjustment needed in this case.
What JDM car has a J32a2?
How would you reflash an stock ECU?