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I believe that with the new salt and pepper shakers, the salt shaker is the one with 3 holes, while the pepper goes in the one with 2 holes. Salt is used more than pepper anyway. Pepper should only ever be fresh ground at the table, meaning salt shakers win out.
If you have an excess amount of mason jars, you can store flour and grains in mason jars. But when you think about how many jars it would take to hold 20lbs or 50lbs of flour, it would be an excessive amount of jars, not to mention the space. You can vacuum seal bags of flour and grains, this will take a lot of bags to do though. If you can afford it, this is one way to do it and ensure it is airtight. 5 gallon food-grade plastic buckets are popular with many people for storing flour and other grains.