Sorry for not writing any sooner, but I have been on the move since arriving on Wednesday.
I went to Ueno Zoo & the Museum of Natural Sciences yesterday and had a lovely time at the Mushisha beetle store. Next on the list is today's visit of Tama Zoo; maybe I can squeeze in the Intermediatheque and the Museum of Parasitology as well today.
As for The Study Room (thanks again for the suggestion): I already went there on my first day in Tokyo. Unfortunately, they are pretty much out of stock of anything related to poisons and venoms; the current dinosaur theme kinda overshadows anything else.

Luckily, the NHM gift shop had a bit more to offer. Many thanks again, though!
The search for animal models to be featured at WdG is way more frustrating than I expected. Kaiyodo's RevoGeo Giant Asian hornet, Giant water bug, Emperor Scorpion etc. are nowhere to be found, and neither are any realistic Gashapon animal models. Akihabara, Nakano Broadway etc. - I have tried them all, and all in all, I have failed to acquire any of the models I was looking for.
To add insult to injury: There were actually three stores that had a few examples of these very products on display. But do they sell them or are they willing to order them? Nope. Which makes you wonder why they display them to the public in the first place...Weirdly enough, I also appear to be unable to get any decent Poison Ivy figurine for the "Poison in Popular Culture" showcase at WdG.
So if any of you reading this knows any other option I could try to acquire at least something like a RevoGeo Giant hornet model during my stay, then please let me know; I'd really appreciate it. Many thanks in advance!
Thanks to the very friendly and forthcoming staff at Mushisha, I was at least able to quench my thirst for Hymenoptera displays.
I'm looking forward to my upcoming Fugu tasting date, the Studio Ghibli Museum as well as visiting the other attractions on my list. Maybe I will be able to make it to the Shinagawa Aquarium, just to see the False killer whale.
Would love to add a visit of the public aquarium of Nagoya (emperor penguins), iZoo or Kawa Zoo as well as Atagawa Tropical & Alligator Park for the ancient Amazonian manatee to the intinerary, but I think that would be overreaching myself. All in all, I'm having a pleasant time in Tokyo.