Well there seems to be a big problem here dude. Here's the situation. There is only one kit made for the MKIII and it has a hard pipe with it. It's meant to integrate right into your stock piping. The part# is 1421-ST001.
This stock port one that they are talking about has a part# of 1421-ST0012. There is no such part#. HKS doesn't have part#'s that are that long. BUT if you take off one of the zeros and use ST012, you have the MKIV kit for the stock port. The MKIV kit is designed to replace the stock port one. The MKIII kit is designed to plug those holes and use a replacement pipe.
I hate to say it, but you bought the MKIV kit my man. Sounds like someone has some false advertisement.
Do me a favor and go look up on the box the part#. I'd like to see which one they sold you.