First off: This is a Most Worthy endeavor because
Crystal Shoes are great for outfits!
When I was doing my Skull Cavern run for the Lucky Ring (same strategy: break crates), it was just loading as many levels as possible and IMO that way is: Stairs down. Depth didn't seem to matter and it really didn't seem like Luck mattered too much
except:
Treasure Chest levels almost always have a lot of crates in them and you get more of those levels with increasing Luck. Plus filthy Trrrrreeeaazzhzhzhsuhhurrrereree!
Since these are all random drops you
could replay the day so only use one Magic Rock Candy until your get the shoes, or if you don't like cheezing the game (I don't) farm Lucky Lunches with some Sea Cucumber Ponds, planting a buncha Blue Jazz, and frankly I just buy Wheat from Pierre to make the Tortillas. You'll get all the Lucky Lunches you need for frequent SC runs.