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This is a real accessibility problem. The line numbers in textpad are impossible to read. What good is it to have the feature and then make the actual line numbers such a faint grey that it is impossible for people with even moderate vision impairment to see them?

How can I fix this?

I need to go to the preferences and change the left margin font for each document class specified.

No, just for the default document. And make sure "Apply these settings to all document classes" is checked.