I feel your pain here, I have had to make similar adjustments to several solutions, best advice I can give you is to use the minimalist theme and customize it as needed, then save your customized theme with a different name and apply that theme to your layouts.
You may need to have more than one version of your customized theme.
Themes are recommended as they are saved one time in the file, if you start to customize individual objects on each layout, you could potentially cause a performance issue due to the extra CSS needed per object/layout and also you could impact performance when rendering each layout as the app will have to apply individual styles to each object, thats why customizing a theme or multiple themes is the best answer.
Please note if you Google for custom themes in FileMaker, there were several "workarounds" used in version 12, please disregard that information as its no longer relevant in version 13/14.
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Alexis Allen has written a good and thorough explanation on how to convert from Classic. She lays out a few options here: http://www.designingfilemaker.com/2015/10/10/converting-from-the-classic-theme-part-1-the-guts/. Converting from Classic can be time consuming, but it is worth it in the long run.