After I reinstalled P3D, aircraft and FSDT GSX then run P3D it complains the FSDT GSX Exclude folder is missing - which it is. I have tried uninstalling and reinstalling FSDT GSX - it does not solve the issue.
This is not normal. The Fsdreamteam\Exclude folder is created by the GSX installer right in the very first step, where it says "Creating Directories", which is before files are being copied.
The only case in which the Exclude folder will be removed during the installation, is if you Cancel it while it's progressing, but in that case you'll see a message saying "Rollback changes", which will undo all the newly created folder/files, resulting in the Exclude folder being removed.
But a normal install will surely create that folder, which will also contain a some files and an empty "scenery" folder.
Be sure the installation completes correctly and, as usual, add the WHOLE Addon Manager folder to the antivirus Exclusions, then run the GSX installer again.