The mod works like this:
- game loads a plant
- mod checks if the plant's id is identical to one in the config; if yes, do change defined properties; if no, do nothing
- game loads next plant, repeat

My mod does not care if the list contains non-existing ids. Neither does it care if plants are loaded with ids not in the list.

The default configuration does not show all the plants, in fact I tried to make it minimal. You can add all the other plant ids you need. There are things to help you.
1) In the start menu is a mod menu that has a couple of buttons to scan and copy properties into the config.
2) Check the mod files, there is a bunch of information.
3) Check the log file. Whenever a plant is loaded, the mod tells you about it. See here "%appdata%/../LocalLow/Klei/Oxygen Not Included/Player.log"
4) Look at the full prefab list here: https://github.com/Truinto/ONI-Modloader-SimpleMods/blob/master/prefab-list.txt (this will be incomplete when new things gets added to the game).

I'm not sure what I'm doing wrong, I have the pre-set to read all and when I go to edit the JSON file, most of the plants are showing up, however I am trying to change to properties of the Pikeapple Bush, but it is not coming on my list in the JSON file. I have looked at the Player.log and it is the first on the list under customize plans, but obviously that is not the file I can edit the properties in.

I have tried to add the plant, with the plant ID, however it just corrupted the file and give me an error message when I restarted the game.

Just checked. It works perfectly fine. What you told me boils down to "it does not work because I make typos in the json file". I don't know what you expect me to do. The changes you do must produce a valid json file. The error message probably tells you exactly at what line and character it cannot understand (e.g where an error is).