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100 Ω sounds like way too much current for modern LEDs. I often end up using 100 kΩ especially for green LEDs. They are very visible under indoor lighting even with 1 MΩ and 3.3 V supply.
For pulling down FETs, you want something in the range of 10 kΩ. 10 MΩ sounds way too high, which makes your circuit sensitive to being touched or affected by moisture, especially if there are near by components connected to the power rail.
My digital electronics grab bag consist of 22 mΩ for sensing, 100 kΩ for battery voltage divider, 22 kΩ for one of the 3.3 V buck converter feedback dividers, 10 kΩ for everything else like I2C pulling.