I've added some LEDs so I can easily check the status of my board. Now I can stop the clock, and step through the code while checking the data and address bus. And I have a few more for the control logic state machine since it takes 6 clock cycles to execute one instruction. I've also updated my 3D models to make it look a little nicer.
Other than more silkscreen to make it pretty, I'm not sure what else is needed. I'm still wondering if I should check some of these individual chips to verify they actually work like I'm expecting them. Sometimes these old datasheets are not verbose in describing the operation of the chips.