I have no great wisdom to offer, just a couple thoughts.
If you have FS9 working, you should have GW3 working as long as it's on the same drive, or in the same partition if you have partitions. That way your registry entries should work for both sims. So I wonder, is GW on the same drive or the same partition as FS9? Does your start link lead correctly to the FSGW executable in the FSGW3 folder? I know these seem like obvious things, but it's so easy to overlook details when moving from one rig to another.
Another thought: did you install GW in the usual way, or just drop the FSGW folder onto an active drive. It's been years, so I don't remember if I had to do a full installation when I copied (what was left of) my old GW into my then-new confutor, but I think I did that, then dropped the remaining contents of the old, developed folder onto the new one. I wish my recollection wasn't so fuzzy.
Anyhow, if you haven't already tried it, starting over from the original GW3 downloads, then dropping in the stuff you have saved from your earlier install, might turn the trick. At least you'd only have to install GW from scratch - all the rest would just be dragging and dropping rather than reinstalling every item individually from scratch.