...is our MKVI setup with a stock intercooler?
If so, where is it mounted?
If not, has anyone added one and noticed large gains due to cooler temps of pressurized air?
The stock MKVI intercooler is sandwiched between the A/C condenser and the radiator. The incoming airflow hits the condenser first, then the intercooler, then the radiator.
I have the APR intercooler along with stage 2. The car is vastly faster, but I can't say how much the intercooler contributed by itself. In general intercoolers help maintain performance, especially on hotter days.
If your car feels faster on a 40F day vs a 90F day, that illustrates one aspect of an intercooler. It cools the intake charge so it's more dense.
APR has a graph on their web site showing it lowers the intake charge temp an average of 35F over stock:
http://www.goapr.com/products/why_mkv_fmic.html
From a bang-for-the-buck standpoint, your first step should be ECU software, such as APR stage 1. Only then consider other engine mods such as intercooler, downpipe, etc.