After talking to Klaude the sub panel is really the best idea. Here is how the sub panel would connect to the main control panel, 2x 2-pin mic connectors, one for each of the two gas valves connect the two boxes.
Inside the sub box, 6x6x4", would be the two S8610U3009 controllers and thats about it. A 3 pin MIC connector connects the sub panel to each valve. Here is a drawing of what it would look like.
This is the box we are most likely going to use. It is weather sealed and the center where we will mount it will be cool enough for the plastic to hold.
And this is a cool connector that is a pass through grommet for the spark wire which we shouldnt splice.