nice touch, you should call that out drag-to-select in the tool tips (assuming i didn't miss it)
on another note, i also appreciate the level advance option, not just for skipping one i can't solve, but also being able to go back to the browser and jump back to the level i am stuck on =)
regarding the UI, throwing this out there because i feel like this game would be nice on mobile:
maybe try expanding the currently selected instruction set with with 8-way arrows, like an arcade stick. the square can act as the toggle since you can't change the primary color, and once you click away, you could compact it down the way you already have it.
not sure if this would be an overall improvement... i usually iterate UX until it feels right, versus being able to visualize an immediate solution. it would solve the size of the hitboxes, though.