Quick answer:
My ride.....
2008 SSV A6 (stock 211rwkw)
2.5 inch stainless exhaust system, 4-1 headers, high flow cats
OTRCAI and mafless tune
Result : 257 rwkw
add:
Stage 2 cam
25% U/D pulley
double valve springs
rods and valves
new mafless tune
Result : 310rwkw
As you have a series II with AFM I assume, you may need to toughen some other internals of the engine due to the AFM and whilst you are at it, get the AFM turned off. From what I'e heard, the AFM engines with some exhaust sound terrible when the AFM kicks in and drops you back to 4 cyclinders. Not sure that new / ported heads will give any significant gains. I looked at this and for the cost circa $3-5k, the power gains weren't worth it for the non AFM L98 donk.
A 3 inch system with be pretty loud and unless you are planning some other mods (i.e FI), the 3 inch system may not deliver any significant gains over the 2.5 inch system except for the db's coming out of it. A 2.5 inch, a nice respectable burble at idle and when driving the burbs, give it the slipper and it's howls.
Change in diff ratio will also add to the total, but start with the initial bolt on's and see how that goes. It's also expensive to do it all at once (unless you've just won Lotto). Whilst getting a tune, get the gear box remapped. It won't add to the kw's but you can tighten up the gear changes to make it drive a little harder.
Good luck with the mods.
Front wheel drive cars are the work of the Devil.