The print $content statement in node.tpl.php is causing my whole layout to break probably due to incorrect nesting of DIVs.
I want to check and fix that but I can't figure out what/where is the source of the $content variable in node.tpl.php file.
I'd appreciate any help. Thanks.
The $content variable in Drupal nodes doesn't come from any one place. All enabled modules are able to add, remove, and tweak the $content variable, using Drupal hooks like hook_nodeapi and hook_view.
Knowing what modules you have enabled and the exact HTML that's causing trouble may help people help you more. As-is, the answer to your question is "it depends".