I think going into Industry is the best bet here. Work for a few years and get a good rec from the boss plus perhaps the 2 you already have lined up. It won't be as glaringly obvious with time in between and a good rec from your current boss.
I think the lack of depth in research and lack of strong letters are the only issues. Perhaps targeting some more schools the next tier down from what you have listed? If the lab you worked in at Columbia isn't leading to success perhaps changing to a different lab?