APR Turbo Back Exhaust and JBS Manifold

[Beetel]

I will be eventually using Custom Code Software,and a JBS hybrid K03 Turbo.
For now I have the basic Giac Software on my 2003 Beetle 1.8T...with just Denso spark plugs,and K&N hi-flow filter (in stock air-box).
There is no other mods to the driveline.
If I fit a full APR turbo back (2.5 inch)exhaust...will it effect current software tune,or have any negative effects...such as bring up any error codes?

Here is link to exhaust:

APR - High Performance Development for Audi, VW and Porsche Vehicles.

Also was thinking of JBS 1.8T manifold...will this work,or fail with current set up?

Here is link to manifold:

Cast 1.8t K03 OEM Upgrade - JBS

Thanx!