I have had very little time to put into the project, but it is still my highest priority personal project. I had to respin both the cart and the programmer board because of errors. But I do have the cart able to store and readback a simple program. Since my gigatron is not correctly running code yet, I loaded the first program the original gigatron ran into the flash cartridge - just simple loads and a jump as recommended by Marcel. I have just finished verifying it on the cart, and need to analyze it running on the gigatron.
I also found a few schematic errors because I did not copy the gigatron project exactly. I fixed those on the gigatron by cutting traces and soldering jumper wires, but that did not immediately solve my problems. So next up is functional testing with the custom code.