stone knife
You asked which would be the better caliber choice for squirrels, woodchucks and to just mess around shoooting paper.
Based on your question, shooting deer falls out of the discussion, it was not asked nor is relevant.
I would think woodchucks have more tenacity for life than a squirrel does since a wood chuck weighs more than a squirrel. If a 36 will handle a wood chuck you have your answer, if a 36 is marginal for a woodchuck, then a 40 is your answer. A 36 caliber ball weights about 63 to 64 grains and a 40 weighs 87 to 90 grains depending on the mold. How much energy is required to do the job
Paper shooting, if it's just messing around, it's a 36 with no wind, if it's more serious paper work, and wind, it's the 40.
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