The car has started up great since I've had it, even after a couple of days with my intake setup. Yesterday it was acting as if it was flooded. It would turn over but it acted like it was getting any gas. I smashed the gas pedal to the floor and held it but no luck. After a bit, it would sputter and I would pump the pedal gently and the car would slowly/roughly come to life. It reeked of gas so I assume it was flooding but I thought S5's didnt have that problem?
I'm gonna put the stock air box back on this evening and take a look at the plugs. Any other ideas?

 

Most 2nd gens have the flooding problems out of all the generations. Stomping/pumping the gas when starting doesn't help. However holding the pedal to the floor (in an S5 only) and cranking will cut fuel. Usefull for unflooding.

 

so flooring it only helps in s5's? Or does it still help in s4's, but only if you full the egi fuse?

 

Flooring it does nothing in the S4's, pull the fuse. In the S5 it cuts fuel so you don't have to pull the fuse. But floor it BEFORE cranking.