If you really want to install this mod on a existing game, it's possible but it require you to do some work with the console.

:: Step zero :: Creating a bat file
Before we start, there is an easy way to type all those commands:
1. Go to your Fallout 4 Game Folder, where your .exe is located.
2. Create a text file, name doesn't matter, we take: BetterPerks.txt
3. Open BetterPerks.txt
4. Now you can do the following, depending on what perks you have picked:
We take for example Lead Belly; Copy paste the following 3 rows:

player.removeperk 00024B01
player.removespell 0004C47E
player.addspell 0004C47E

This will remove the perk Lead Belly 3, removes and re-adds the spell provided by Lead Belly.
Simply copy and paste the console command + ID and you will save a lot of time typing!

Removing all perks that are no longer covered will look like this:
player.removeperk 001D246A
player.removeperk 00065E4B
player.removeperk 00065E4C
player.removeperk 00024B01
player.removeperk 00065E0C

5. Save your .txt file and go ingame, open your console and type:
bat BetterPerks.txt

Fallout 4 will now automatically read the text file and will execute those commands.

:: Step one:: removing non existing perks
*You only have to remove the perks you have picked!
Get rid of the following perks, which are no longer provided by this mod:
Type into the console:

player.removeperk xxxxxxx
(replace xxxxxxx with the number of the regarding perk listed below)

Example: player.removeperk 001D246A  - removes Locksmith Rank 4

----------------------------------------------------------
List of perks that are no longer existent
Name_of_the_Perk - ID
----------------------------------------------------------
Locksmith Rank 4 - 001D246A

Refractor Rank 4 - 00065E4B
Refractor Rank 5 - 00065E4C

Lead Belly Rank 3 - 00024B01
*Note:
If you have picked Lead Belly Rank 3 type this:
help "Lead Belly" 0
There will be a Lead Belly Perk with some those digits: xx000804
type again and replace xx with numbers you see in your console: player.addperk xx000804

Chem Resistant Rank 2 - 00065E0C

----------------------------------------------------------

:: Step two :: re-adding spells
*You only have to re-add spells for perks you have picked!

two commands are necessary:
player.removespell xxxxxxxxx
player.addspell xxxxxxxxx

Example: player.removespell 0004D871- removes Action Boy/Girl Spell
Example: player.addspell 0004D871- adds Action Boy/Girl Spell

----------------------------------------------------------
List of spells that have to be re-added when the specified perk was picked
Name_of_the_Spell - ID
----------------------------------------------------------

Action Boy/Girl - 0004D871

Quick Hands - 00127561

Lead Belly - 0004C47E

Solar Powered - 0004D8A9

Tougness - 0004A0AD

Rad Resist - 001FA241

Rooted - 001D2481
Rooted Rank 3 - 00097344
----------------------------------------------------------

:: Done! ::