I also wanted to make a computer in a logic simulator. However, I found http://www.cburch.com/logisim/ was good enough for my needs. It allowed me to create a 16bit simple cpu and run it at about 4khz. You can even create custom components in javascript so that things like memory modules aren't just giant arrays of simulator-time wasting flip-flops.

Unfortunately, logisim has been abandoned by its creator