Sounds like the new wcs you created is wrong.
I think there may be a way to adjust it but honestly I'd be more likely to create it again (correctly this time) and then just delete the bad one.
If you're having trouble getting it oriented the way you want, use the 2 line method. Create a line starting at your desired origin in the direction that you want X+ to be. Do the same for the Y+.... Then create a WCS by "geometry" selecting the 2 lines (always grab X first) and your wcs comes out perfectly oriented every time.
You'd probably really like the Dynamic WCS feature in X4. It simplifies this process a bit.