I am not seeing anything in the log to indicate a MO2 problem. It looks like this install is a global instance of MO2, by this path "C:/Users/Desktop/AppData/Local/ModOrganizer/1/crashDumps)". Can you provide the paths to the Base directory, Mods directory and Profiles directory or even better a screen shot of the paths tab of the configuration settings dialog.
I would ask that you go into the "My games" folder and look for the SKSE folder and delete the log files there and run the special edition loader again, shut down the game and post the logs that are created.
You can also try and create new Skyrim.ini and SkyrimPrefs.ini by deleting them, backup the originals first, and run the game from steam to generate new inis.
Then in MO create a new test profile without any mods enabled and see if the game will start. If it starts, then enable your SKSE mods one at a time and run the game to see what happens.