Use tools like DiffMerge or WinMerge to compare the old and new files and redo the changes. You will spend probably an hour doing this but not more, specially if you have made changes only to a few select files. The settings data will stay and hence Custom CSS entered into theme options should be fine. It’s always a good idea to have a backup though. Hope this helps.
Best way to protect yourself from theme updates is to always make changes in the child theme. The theme is mostly child theme friendly and hence when you have time, you can probably go through the changes you have made to the core theme files and try to move them to child theme so that the core files are not affected and upgrades are smoother.
It is safe to upgrade to 4.0 and you can upgrade to WordPress 4.0 and then to Agile 3.0. Make sure you enable visual composer when you activate the latest version of theme (just follow the prompt at the top of the admin page).
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