If you're going for 100% completion in story mode to hunt easter eggs, the best way to track your progress is via the Rockstar Social Club.
If you sign up and connect your PSN ID to your Social Club login, you'll be able to track your progress in real-time via their website. There's a percentage there that is kept up to date while you play.
For 100%, you need to complete:
- All missions, including assasinations. I believe there are 69, but it may vary depending on your choices during the game (ie, heists especially)
- 42 hobbies. Some hobbies are optional for 100%, there are 59 total.
- 20 strangers and freaks. There are 59 total, so there are a lot of optional ones.
- 14 random events. This is the only one where it doesn't matter which ones you complete.
- 16 "misc" activities of 30 total. This includes spaceship parts, letter scraps, knife flights, stunt jumps, and under the bridge stunts - all of them.
Since not everything counts and it can be hard to keep track, the Social Club is a lifesaver. It even has a map that lists the collectibles, the random events, and the strangers/freaks.
They don't track the stunts (knife flights, stunt jumps, under the bridge) so you'll need to track those yourself, lest you lose track and forever be missing one.
The Special Edition and Collector's Edition games both come with a special code that is applied to your account. This applies to any PSN/XBL profile that you link with your Rockstar Social Club account. As a result, there will be no change to your progress in GTA Online.
Single Player progress is local to your game console. Unless you change consoles in the process, such as upgrading to the PS4/Xbox One, there won't be any loss of save progress.
For example, I purchased the Special Edition of GTA V on the Xbox 360 on launch day. I quit playing the game after a few months, but got the game with the PS4 Black Friday bundle. After linking my Social Club account, I still have access to all of my Special Edition content.
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