The Ergodox split keyboard is designed for exactly this arrangement. Both the hardware and firmware are freely licensed, allowing for easy customisation. The design features a large cluster of keys under the thumb position, allowing for ergonomic use of modifiers - no more emacs pinky.

The CAD files are available at Ergodox.org if you'd like to build your own, or you can contribute to this crowdfunding campaign to receive a preassembled keyboard:

https://www.indiegogo.com/projects/ergodox-ez-an-incredible-...