From there, I want simple routines to be able to detect where the mouse cursor is and/or if the keyboard is being used, and from there flick bits on and off in the video array to form pictures.

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I would do this as follows:

1. thread/process one, real user interface that maps X api calls to memory mapped IO in block of memory.

2. thread/process two, a CPU emulator that just continually runs the fetch/execute cycle using the same block of memory as it's address space.

3. Signals delivered to the second process I mentioned count as interrupts to the processor, eg the signal handler causes the emulated CPU to emulate an interrupt

4. the UI thread/process responds to notifications from the CPU thread/process.

5. In the CPU thread/process everytime a memory access occurs on a guarded piece of memory notify the UI process, this can be done by doing an AND/XOR on every address to which a write is done, if the result is zero then signal the UI process.

This could either be done as a single process with two threads, or a pair of processes with shared memory to act as the memory space of the emulated CPU.