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If all the other chips are correct you don't need additional registers. This is because both the CPU and RAM have registers internally, which break the cycle (ROM is a combinational circuit).
Putting additional registers will create problems, because the computer is supposed to do specific things at each clock and the registers will delay these to the next clock.
Make sure that all the components work properly. Many of the chips have built-in variants, which are both much faster and better tested than. For example, if you don't have a file named ALU.hdl in the same folder as CPU.hdl, then the built-in ALU will be used. Conversely, if you do have such file, it will be loaded and used in the CPU. Try moving away all .hdl files except Computer.hdl, CPU.hdl and Memory.hdl and try your tests again.
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