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#2 You can completely edit theme.html and the other theme files. However, the default theme cannot be edited. If you want to use the default theme as a starting point, you can duplicate it and give it a new name. (Note: You will need to edit theme.html to point to the new directory instead of "default" directory. Search on the word "default" in your new theme and you'll find a few occurences you need to update).
#1 If you can find the template for headlines, you can edit it to include target="_blank" or whatever window technique you choose. You must first "clone" the default templates and give the template set a new name... then edit the custom templates you have created.
I hope that helps.