searching file A for any and all whitespace/tabs/commas then replacing these occurances with commas

That doesn't sound right to me! You're going to replace all the commas with commas?

What if your file looks like:

foo[tab]bar[tab]baz
foo[tab]bar, or possibly baz[tab]quux
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You need to enclose the second item in the second line in quotes:

foo,bar,baz
foo,"bar, or possibly baz",quux
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or else your data isn't going to be right.