Would you mind putting a link or some steps to recreating what you've done on th 3DS?
Chowdren is the way to go. Chowdren is a custom runtime built for games like Iconoclasts (also made in Construct), created in C++. You can contact the creator and they'll help you export your game to C++ (Native)
So, if you read into it, you just have to sign up for the developer program, sign the NDA, and you'll be granted access to the SDK. After you've finished going through all that, you can export and compile your game for the 3DS.
link to page explaining this:
Link to the Nintendo Developer Portal:
What this means for you is, you really just need to be modest with the scale of your project. Make sure you're working within the hardware's limitations, and you can continue to develop your project until you're prepared to port it to the 3DS. Of course, you'll need to find a way to support 3DS controls, but I'd simply suggest that if you speak to the developer of Chowdren, just ask them to map the input received from the 3DS SDK to the Gamepad & Touch objects.
I guess another thing you'll have to work out is the two screens. I'd suggest making each screen display a different layout, then make Bottom Screen Layouts and Top Screen Layouts. That'd simplify it quite a bit. This might actually be how the Wii U plugin worked, but I can't remember, it's been a long time since I've used it.