The Skyrim Perk Utility allows you to set (or reset) which perks you have active, via a script that can be downloaded. This utility will use natural progression as if you took the time to get the perks yourself.

Access the utility here: Skyrim Perk Utility

Press the ~ key while in game to access the console.  Then type the following

bat <filepath>/<file name>

The game will begin to add the perks from the file. Give a few seconds to a minute for all of the script to load into the game. After you executed the scripts your character should have your desired abilities. The scripts change your level and perks, but don't change your attributes i.e. magicka, health and stamina are not affected. If you want to change them you could use the console command "player.setav health 500" etc.

Pull requests welcome!

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Please do not fix more than one issue at a time. Your pull request should only fix what is described in this issue.