Just came here to rant about:
I can’t for the life of me get the first two down in my memory. I honestly think I have SRSed the wrong meaning into my brain. Every….single……..time……………I get it wrong.
Arg….
You have my sympathies, these are tough 
Coincidentally, the current intermediate book club pick is great practice for all of these!
Frankly I would just use “undo” to pass those as long as you remember that it’s police-related. Assuming that you don’t currently live in Japan, you’ll almost certainly have forgotten the distinction by the time you need it, if that time ever comes.
I just set a synonym for all of them as ‘police.’ Then you know it’s police related but can learn the actual difference whenever you interact with native material later.
If it helps, 警視庁 refers specifically to the police force of Tokyo - WaniKani renders it as “Metropolitan Police Department” because that’s its official name in English, but ultimately it’s just the Tokyo prefectural police. Maybe you might consider adding a easier-to-remember synonym.
Meanwhile, the 警察庁 is basically just an oversight comittee for the various prefectural police forces - aside from its control of the Imperial Guard, it has no operational units of its own whatsoever (though it can assume command over any prefectural forces in the event of an emergency or disaster). Odds are pretty good that you’ll never come across this even in day-to-day life in Japan.
I have similar catch-all synonyms for baseball terms and military titles. I had an “a-ha” moment when I realized that I don’t actually know the difference between a lieutenant, general, and wing commander in English so why would I bother learning them in Japanese?
I do get some mileage out of knowing the 尉→佐→将 hierarchy because it comes up regularly in the fiction I consume, although I certainly don’t know the specifics of what each rank means exactly, nor do I care.
Well, I know 将軍, but that’s a freebie.
This is the way..
I also don’t bother learning plants/flowers anymore than that’s what they are. If I can’t make a distinction in English, being able to know it as belonging to a category is enough for me.
Soggyboy’s solution of setting “police” as a synonym seems to be the way to go.
When I moved to Germany several decades ago, I didn’t know how the police were organised here either. I certainly didn’t know the terminology. Maybe after 10 years I understood the system generally, but I probably wouldn’t have been able to write their various names correctly. It was not a problem.
Maybe in Japan, you might interact with the guys at the koban on occasion. I hear they can be helpful.