Lukterran, since you're thinking about re installing your Steam download, you might want to look at this
thread over on the SubSim "SH4 Wolves of the Pacific" forum section.
This last post, from new SubSim member dodougla, may help in placing your game in a folder other than Windows "Program Files (x86)".
As a matter of fact, there are several posts around here that get into how to work with the Steam download. Maybe a search would pull them up. Might be worth your while to look at the Steam Forum as well. I'm wondering if Steam puts Registry entries onto ones system too, making it hard to remove some files that need to be re installed??
I'm suspecting your DirectX version 11.2 is fine. Just let the game wizzard do its thing when you set up what the game should install with regards to the DirectX v9.0c. DirectX will decide what it should add (if anything) to your newer version.
One thing you won't need to add within the install wizzard is the "Game Shadow" part......I guess the Steam version of the game contains this?? The DVD version does. You don't need it, and really you don't want it either!