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I'm trying to create two (for now) sites in multisite WP installation that use same theme, but require somewhat different functionality i.e homepage has a bit different layout and there will be some CSS changes.

Is there a way that I could use to override functions.php and other theme files for each site?

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I would recommend a Parent/Child theme for this. Read the section linked below for a good example of making functions within your theme pluggable.

http://codex.wordpress.org/Child_Themes#Using_functions.php

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Since you can use different themes for the same multisite installation you can create a new theme folder which will basically be the same theme. Just activate this newly created theme via dashboard and you are ready to go.

Then you can completely customize your theme from website to website without any problems.

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