Well I finally got around to re installing FSGW, but I have ran in to a small problem with FSGW and TrackIR. It has something to do with the language.dll for FSGW. TrackIR worked fine until I ran the GWUP1 and GWUP2 updates. After the updates TrackIR stopped working, so I copied and pasted the language.dll from FS2004 in to FSGW, now TrackIR is working, but FSGW is using the saved flight from the Flight Simulator Files folder and not from the Golden Wings Files.
This is a slight annoyance and I'm sure I will fine a work around for this, but I was hoping maybe someone here has had the same problem and found a fix other than using FS9's language.dll.