Well, the short program did not execute as predicted.  The program got stuck constant executing a jump instruction back to the same instruction.  This makes sense if most of the memory is filled with all 1s - FFFF.  I could see both clocks running.  I will have to manually step through the instructions by controlling the clock.  Or manually feed instructions to verify they are being decoded correctly.  I know it is jumping because the program counters are being loaded, but I'm not sure if the correct location is being loaded. 

I will also need to check to see the initial state of the Y register.  I assume it is powering up as all 0s.  If it powers up as all 1s, then when it gets to the branch instruction, it will jump to 0xFF00 instead of 0x0000.  I wonder if maybe I should add one extra instruction to load the Y register with 0x00 to ensure it will jump back to 0x0000.  I believe the machine instruction is 0x1400 (ld [D],Y) which I will put in address 1 so the new program would be:

  byteProgram(0x0000, 0x0000);
  byteProgram(0x0001, 0x1400);
  byteProgram(0x0002, 0x0002);
  byteProgram(0x0003, 0x0003);
  byteProgram(0x0004, 0x0004);
  byteProgram(0x0005, 0x0005);
  byteProgram(0x0006, 0x0006);
  byteProgram(0x0007, 0xfc00);
  byteProgram(0x0008, 0x0008);