You are keep getting error message that you shouldn't get, and that nobody else reported. The scenery.cfg issue, for example, simply shouldn't happen.
Unless your scenery.cfg was ALREADY corrupted, but if this is the case, you should have got an warning by our installer and if this was the case, the installation hasn't completed, and it will not, until you fix your scenery.cfg from any errors.
If you haven't seen any warning from the installer, either your scenery.cfg got corrupted after the installation OR, again, you ran the installer when FSX wasn't properly closed, which always creates problems with files. As I've said, if FSX has problems properly closing on your system, it's safer to run any installation after a Windows reboot, without launching FSX first.
Also, you forgot a crucial antivirus step: if your antivirus wrongly identifies any of our software as threat, turning it off during installation is only ONE step, but it's NOT enough, you should also configure it to exclude the following files:
YourFSXfolder\bglmanx.dll
YourFSXfolder\fsdreamteam\Couatl\couatl.exe
from scanning, BEFORE turning it back on
I checked PHNL under the addon-manager and PHNL was active which meant I never de-activated it before reinstalling
This means the Addon Manager is runnig, but Couatl is not. Which is a problem. Both should run. In any case, you will never lose your Activation, regardless of what you do, unless you reinstall Windows.
The fact that Couatl is not running, is probably because you missed the antivirus config step.
Now, you should probably redo it again from scratch, without missing the antivirus configuration step.
Check you don't get any scenery.cfg errors before installing again, exit from FSX cleanly, and reboot Windows before reinstalling again.