Final update: I have changed the code so that when you add a new plant, or edit an existing one, the system will automatically correct any abbreviations that may be non-standard.
So if you try to add a plant with a species of, for example, "foo ssp. bar" then the system will auto-update that to read "foo subsp. bar".
The same with synonyms and editing plant names. So this should resolve that once and for all.
Now, there are a few oddball plants still in the system that weren't found but that I know are there. For one, some of the alliums have "var.foo" where foo is some var. name. My script couldn't catch it because there was no space after the period.