I have yet to test out the latest update, due to not wanting to break anything further, but from the looks of it, the latest version of ACF should have resolved the issue.
Since I really needed a fix, the day I posted on this thread, I decided to use TinyMCE Advanced ( via http://wordpress.org/plugins/tinymce-advanced/ ) as a work around to the issue stated above.
TinyMCE brings back the WYSIWYG options that are removed.
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Download Latest Version: ACF 4.3.8 http://downloads.wordpress.org/plugin/advanced-custom-fields.zip
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ACF Change Log as of 05.07.2014
4.3.8
Validation: Fixed disabled button issue in WP 3.9
4.3.7
WYSIWYG field: Fixed missing tinyMCE buttons in WP 3.9
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Lost the HTML button as well, but so far, no luck in getting the issue resolved. I updated to the latest version, via the link above, and the “HTML” button on the sink WYSIWYG has yet to show up.
Same issue here as well. Best of luck Elliot, seems like this WordPress 3.9 update is a nightmare so far.