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So I was wrong, and it turns out Faust is the organization rather than a the person Banjo was framed for killing. (In my defense, they straight up said the guy's nickname was The Devil's Scientist)

What's more Blood Stark appears to be the same rank as Night Rouge. He also seems to be a new character, since his response to Night Rouge's questioning felt way too relaxed for compared to what Night Rouge's regular lackey would say.

Next, it seems that Nabeshima was the host for the Mirage Smash and the Square Smash. More importantly, their essences probably make the Full Bottles needed for Build's NinninComic form.

Also, I thought Nabeshima's memory loss was going to hint that being turned into a Smash twice will erase more of your memories, but the dialogue at the beginning with Night Rouge seems to imply that this is the first time Faust has tried this, and Blood Stark said complete memory erase comes from the new process they're using.

Lastly, Soichi (the café owner) being a member of Faust actually seems pretty unsurprising looking back; He told Ryuga and the audience that something big happens upon collecting all the Full Bottles. He was the one who suggested Sento become Build and fight the Smash. He even has a daughter who can purify the Full Bottles Build obtains from Smash (an ability I'm pretty sure girls don't usually have).
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On a side note: Man, that wall panel became really important to the plot rather quickly.
Episode 3
Ryuga: Hey what's this thing in your wall?

Owner: Oh, we used to use it to find Best Matches.

Episode 4:
Sento: WHY THE F@#K DO YOU HAVE THIS PANEL IN YOUR WALL?!

Owner: Well...