The only thing IF does, as you all know, is start P3D from the command line passing in the flight file as the argument, just as we do when we select an fxml from within Explorer and choose Open with P3D from the menu.
The sim must be able to start from a .fxml file without crashing, so this suggests that the sim is still at fault in some way and I would presume it remains non-stock. This comes up from time to time due to a faulty installation of an add-on.
The best thing to do is delete all the folders properly and install P3D fresh. When the sim starts correctly from the Fly! button in IF we know for a fact the sim is good. From that point we can install add-ons.
When the sim can be indexed and the sim can start with the fxml then we know the sim is working OK. In these cases it is Ideal Flight that is showing us the sim has an error condition that must be resolved.
This is what I would do:
1/ Install P3D fresh in new folders.
2/ Run Ideal flight, ensure the index is ok and that the sim can be started from IF.
3/ When that is working add the modify allow permission on the LM folder Users group with explorer before installing any other addons.
Generally it is some permissions issue in P3D addons that cause problems. However, very often, users attempt to avoid those issues by installing P3D in a private folder. That method is not so good because the folder is owned by the user, not the system. That can cause issues with some addons that install files into P3D for example - which is a major problem inherited from FSX style addons.