Put both in the steam folder and named the clean one "Grand Theft Auto V - Clean"
and then remove the "- Clean" or "- Mod" from the one you want to play (https://gyazo.com/14fcd599b6cea3bb9956c97b5f563a34)
As you see in the picture, I have 3 GTA V versions:
Clean
Modded
1.27
If I want to play, let's say, the modded one, I remove the suffix from it so it becomes
"Grand Theft Auto V"
as in this picture: (https://gyazo.com/3385e263599069f2abe961fed9681c3e)
The ".modded" is gone from the folder, so now I can run it from steam as Steam will only look for the one with "Grand Theft Auto V",
Now if you wanna play the clean version, do the same but with the clean one.
(https://gyazo.com/411cde2583603112b89d054e2f42ba87)
Now let's say I want to use the 1.27 one, the version used for speedrunning the game, I do the same as I did with the other two.
(https://gyazo.com/2b8c276107d40be49d79181e2dc52499)
Note: for 1.27, you need an older version of Rockstar Social Club installed, there are tutorials on youtube and speedrun.com/gtav
Hope this helped.