WordPress Doesn't Work On Certain Pages Anymore

Question

We were having some issues with inline javascript, so we decided it would be wise to modify the add-filters file by commenting out the line associated with wpautop and the_content. After uncommenting the line, it seems that some of the pages don't want to revert to having paragraphs (generally the index pages). Any ideas as to how this problem can be worked around?

Here's a snippet of some of the parts that are not being formatted:

<div class="blogContentText">       

    <?php
        global $more;
        $more = 0;
    ?>
    <?php echo strip_tags(get_the_content(__('<br>[Read more...]')), '<p><a><h2><blockquote><code><ul><li><i><em><strong><h4>');?>

</div>