The 3.0tfsi already has a front mount cooler, well heat exchanger to be correct, an intercooler in more for turbo applications and is air to air. The S5 is air to water.
I don't know of any issues, it's quite a simple set up, so don't see why there would be any issues.
What year is yours as they were revised in 2014. I have done the free 100% default run mod. Basically being able to disconnect the ECU control of the charger coolant pump. When the ECU feed is disconnected, it will run the pump at 100% constantly and also run on for 30 seconds after engine shut down. It will also run fro 30 seconds when opening the car! I have put tails with spade connectors so I can connect or disconnect quickly. I had mine rolling roaded with this mod and at idle it was 43 degrees inlet temp which dropped to 38 degrees when running on the RR.
You only need the oversized charge cooler when at stage 3+. If you have stage 2, remap and crank pulley, then it will be pointless, unless you live somewhere with a hot climate?
I don't sorry. But it's the yellow wire with the blue tracer that goes into the plug on the pump. I basically cut into that and connected some etc wires in so I could unplug it at a more convenient location, ie just behind the headlight. You can add longer wires and feed into the car for an internal switch.
I keep it connected and only disconnected for the rolling rolling road. Not disconnected since!
I did this mod today,very easy if you dont want it switched as it only requires the cutting of 1 wire. The wire is Yellow/blue on my 2010 & according to the below it is the same on a 14 (thanks to @beans912 for the diagram )...