Try searching the community layouts for "Brain's Starsector Layout."
It uses the left stick for numbers, click to select, and the left shoulder mode switches the d-pad, face buttons, left stick, and touch pad to various other functions. Also, double click L5 for alt (which transfers inventory items when you mouse over). You may need to increase the interval on that one, as I had trouble clicking it fast enough when I first started using it, but it will vibrate when it does switch to alt.
You may have to modify a few parts, but I would warn you Steam Input has always been a bit broken, especially when using its more complex features. Some settings may overlap, and you'll have to delete the setup you're using. Just start fresh again and quickly change to what you want without fiddling around too much.
The problem appears to be old settings aren't really deleted when you change to something new, and it can overlap in strange ways.
