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I'd find out the CSS class that MathJax gives to each of the equations and then write a rule in your CSS file so that it has the size that you want. E.g., I think the separate equations have the class "MathJax_Display".
My textbook has the MathJax blocks appear much smaller compared to the MathJax inline portion. A particularly good example if this is [here].(http://prob140.org/textbook/chapters/Chapter_04/04_Updating_Distributions)
How can I scale the MathJax blocks without scaling the inline text?
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