Well after getting frustrated with GWX not wanting to work beyond September of 39 I took a bit of a break from trying to fix this. Fast forward to about half an hour ago when I downloaded a mod for Civ 4 BTS and it wouldn't work I decided to check something. I wanted to see if the Civ 4 folder had all the security permissions checked to yes and lo and behold it didn't, so I checked them to yes and the mod worked. That suddenly got me thinking, "What if I move my SH3 folder to the X86 and then make sure all the security permissions were checked to yes. Would GWX finally work after the month of September was over"? Well I did just that and guess what? IT FINALLY WORKS!!!!!!
Now all that's left is to download the GWX3 files for SH3 commander, do the same thing to its folder and see if that also works. I'll post and update on whether it does or doesn't.