I made a cable that has all the available signals from the SNES output on it connected. I was fortunate that the SNES RGB connector cable I bought had all the pins populated, so I just had to hack it up and solder some wires to it. I terminated the other video signals with an RJ-45 connector. Here is the description of what I have currently:
EDIT: Removed no longer used.
I also got myself a scope and tested the RGB output channels. I made a basic test program to test maximum output levels. It looks like max of 170 mV for full 5 bits set color, which seems pretty low (I see 660mV online for RGB signals) (EDIT: I had attenuation settings wrong, its actually ~1.5 volts.). For real world testing I captured some waveforms and the results are kind of interesting. Rise times are pretty slow compared to pixel clocking rate. One pixel lasts ~200 ns and rise times can be approximately that long. Obviously this still works as the RGB output channel is used regularly but this something to keep in mind when comparing pixel color emulator. Here is a sample:

I still have the option to tap the digital RGB on the ppu, but I would really prefer if I didn't have to touch the console so I will press on with this for now.
Now I need a clock source, split the csync signal, and to convert to digital color.