Your biggest power adder would be a custom intake. I think that the lower part of the factory one could be modified to be passable, but the upper part has to go.
I would recommend not using S4 parts, but S5. The rotors have better compression and are lighter.
What power levels are you looking for?
I have heard of an Aux Port Bridge, which will help the high end appreciably while maintaining some semblance of low end torque (not a bridge port until the sleeves open).
Unfortunately, I have never had the opportunity to build a maximum effort 6-port, but my mildly ported 4-port has 60 WHp and 60Wlb-ft on the best 6-port build I had (Haltech E6X, stock - polished intake manifold, port matched with custom cold air intake - no AFM, stock S4 block), Racing beat headers,
4-port vs. 6-port
216 WHp vs. 155 WHp
160 Wlb-ft vs. 100 Wlb-ft.
Short story is the the 4-port has a lot more potential than the 6-port.
The 4-port loses torque in the high revs because the stock ignition is weak past 6,000 RPM. The charging efficiency on the 6-port is so low that the ignition is plenty for it.