The bootloader is not absolutely necessary because you can use Sketch > Upload Using Programmer to upload to the microcontroller using an ISP but of course it's very useful and it's quite easy to build optiboot for many parts.
The one essential thing is the boards.txt file. You may also want to create a variant file(pins_arduino.h). There will likely be some porting required if you want to use certain core or library functions.
You can use Arduino AVR Boards as a reference as well as 3rd party hardware packages. I like hansibull/MCUdude's cores(MCUdude (MCUdude) / Repositories ยท GitHub) they would probably make a good model.
I probably wouldn't end up using an ATmega406 but I like to see support for more parts added to the Arduino IDE. This could be a valuable contribution to the community if you release it publicly. If you do so please consider taking some time to add proper documentation. The time spent will pay off in the end, not only in making the project accessible to more users but also reducing the amount of support requests.