You have a problem with the change of the template. From the phtml file you need made the $this->getChildHtml() corresponding. If you go to your old template in app/design/frontend/base/page/3colums.phtml for example you can see the next command lines:
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="<?php echo $this->getLang() ?>" lang="<?php echo $this->getLang() ?>">
<head>
<?php echo $this->getChildHtml('head') ?>
</head>
<body<?php echo $this->getBodyClass()?' class="'.$this->getBodyClass().'"':'' ?>>
<?php echo $this->getChildHtml('after_body_start') ?>
<div class="wrapper">
<?php echo $this->getChildHtml('global_notices') ?>
<div class="page">
<?php echo $this->getChildHtml('header') ?>
<div class="main-container col3-layout">
<div class="main">
<?php echo $this->getChildHtml('breadcrumbs') ?>
<div class="col-wrapper">
<div class="col-main">
<?php echo $this->getChildHtml('global_messages') ?>
<?php echo $this->getChildHtml('content') ?>
</div>
<div class="col-left sidebar"><?php echo $this->getChildHtml('left') ?></div>
</div>
<div class="col-right sidebar"><?php echo $this->getChildHtml('right') ?></div>
</div>
</div>
<?php echo $this->getChildHtml('footer') ?>
<?php echo $this->getChildHtml('before_body_end') ?>
</div>
</div>
<?php echo $this->getAbsoluteFooter() ?>
</body>
</html>
Ok, then you be careful with this, all block in yout template need a getChildHtml() from the corespondig phtml. In your case is probably that you don´t add this call from the template.
Then don´t work head, content, footer, etc.
I think this is your ploblem, nonetheless you can write the content of your custom template to help you with the solution.
Hope help you