I have tried adding a .json file manually, using an edited copy of the wheat recipe, only changing the input seed, and output item.

{ "type": "botanypots:crop", "seed": { "item": "mysticalagriculture:certus_quartz_seeds" }, "categories":["dirt"], "growthTicks": 3, "growthModifier": 1.2, "display": { "block": "mysticalagriculture:certus_quartz_essence", "properties": { "age": 7 }
That is what I have in the top of the file that I named certus_quartz.json, and I have tried various names for the .json file.

Is this me?

I added the following

"conditions": [ { "type": "forge:mod_loaded", "modid": "mysticalagriculture" }

and it still is not working

You are missing two closing curly brackets in your first code sample and a closing square bracket in your second code sample.

I would suggest starting with one of the existing Mystical Agriculture recipes, such as nether_quartz.json.

Consider just using the one that @Warbringer12 already made.

The PR that was mentioned has now been merged.