You can narrow down what the problem is by simplifying things. Doing too many changes in one go is a common programming mistake because it makes it really hard to narrow down exactly why something isn't working.
Basically, start with a version that's exactly the same as some text-book example, e.g. copy tomato fruit from the tomato raws exactly and add it to your plant. Test that first without any changes. So the first step is to add tomatoes or some other known working fruit to your plant.
Then change A LITTLE at a time (ideally just one token at a time), and test each change until you have the desired outcome, or identify the problem. Make sure you keep copies of your "best so far" raw version so that if some single change screws the whole thing you can go back and try something else without losing the bits you did fix.
Don't assume all combinations of tokens will just "work". e.g. you've got the output item type as ROUGH:NONE, try setting that to GROWTH_ITEM:PLANT_GROWTH:NONE and see if that's the issue. Stockpile rules can be fickle in how the categorize different materials, and you have to workaround the limitations. If it is, then you have to find another workaround to get it into gem form and get it properly stockpiled.