The Graphics Compositor & SFX coprocessors would be primarily programmed by the Output Unit using compiletime constants. As would the Arithmetic Core, with the aid of a special "label" type.
To aid debugging that Arithmetic Core I'd probably end up creating a tool which has the Input Preprocessor emulate its RAM, triggered by user input or a periodic timer. So we can stepwise debug the program, and view its entire state! As well as a disassembler rendering arrows for control flow.
2/3?
alcinnz