Figured it out. All done in the index.php file
Stating around line 100. I added the % for all 4 positions
if ($this->countModules("bottom_row_one_1") && $this->countModules("bottom_row_one_2") && $this->countModules("bottom_row_one_3") && $this->countModules("bottom_row_one_4")) { $bot_row_one="24.9%"; }
else if (!$this->countModules("bottom_row_one_1") && $this->countModules("bottom_row_one_2") && $this->countModules("bottom_row_one_3") && $this->countModules("bottom_row_one_4")) { $bot_row_one="33.3%"; }
else if ($this->countModules("bottom_row_one_1") && !$this->countModules("bottom_row_one_2") && $this->countModules("bottom_row_one_3") && $this->countModules("bottom_row_one_4")) { $bot_row_one_1="49.9%"; $bot_row_one_3="24.9%"; $bot_row_one_4="24.9%"; }
else if ($this->countModules("bottom_row_one_1") && $this->countModules("bottom_row_one_2") && !$this->countModules("bottom_row_one_3") && $this->countModules("bottom_row_one_4")) { $bot_row_one="33.3%"; }
else if ($this->countModules("bottom_row_one_1") && $this->countModules("bottom_row_one_2") && $this->countModules("bottom_row_one_3") && !$this->countModules("bottom_row_one_4")) { $bot_row_one="33.3%"; }
else if (!$this->countModules("bottom_row_one_1") && !$this->countModules("bottom_row_one_2") && $this->countModules("bottom_row_one_3") && $this->countModules("bottom_row_one_4")) { $bot_row_one="49.9%"; }
else if (!$this->countModules("bottom_row_one_1") && $this->countModules("bottom_row_one_2") && !$this->countModules("bottom_row_one_3") && $this->countModules("bottom_row_one_4")) { $bot_row_one="49.9%"; }
else if (!$this->countModules("bottom_row_one_1") && $this->countModules("bottom_row_one_2") && $this->countModules("bottom_row_one_3") && !$this->countModules("bottom_row_one_4")) { $bot_row_one="49.9%"; }
else if ($this->countModules("bottom_row_one_1") && !$this->countModules("bottom_row_one_2") && !$this->countModules("bottom_row_one_3") && $this->countModules("bottom_row_one_4")) { $bot_row_one="49.9%"; }
else if ($this->countModules("bottom_row_one_1") && !$this->countModules("bottom_row_one_2") && $this->countModules("bottom_row_one_3") && !$this->countModules("bottom_row_one_4")) { $bot_row_one="49.9%"; }
else if ($this->countModules("bottom_row_one_1") && $this->countModules("bottom_row_one_2") && !$this->countModules("bottom_row_one_3") && !$this->countModules("bottom_row_one_4")) { $bot_row_one="49.9%"; }
else if (!$this->countModules("bottom_row_one_1") && !$this->countModules("bottom_row_one_2") && !$this->countModules("bottom_row_one_3") && $this->countModules("bottom_row_one_4")) { $bot_row_one="100%"; }
else if (!$this->countModules("bottom_row_one_1") && $this->countModules("bottom_row_one_2") && !$this->countModules("bottom_row_one_3") && !$this->countModules("bottom_row_one_4")) { $bot_row_one="100%"; }
else if (!$this->countModules("bottom_row_one_1") && !$this->countModules("bottom_row_one_2") && $this->countModules("bottom_row_one_3") && !$this->countModules("bottom_row_one_4")) { $bot_row_one="100%"; }
else if ($this->countModules("bottom_row_one_1") && !$this->countModules("bottom_row_one_2") && !$this->countModules("bottom_row_one_3") && !$this->countModules("bottom_row_one_4")) { $bot_row_one="100%"; }
In the module position I added the new width name:
<?php if($this->countModules('bottom_row_one_2')) { ?>
<div id="s5_bottom_row_one_2_mod" style="width:<?php echo $bot_row_one_2 ?>">
<div id="s5_bottom_row_one_2_inner_mod"<?php if($this->countModules('bottom_row_one_3') || $this->countModules('bottom_row_one_4')) { ?> style="padding-right:14px"<?php } ?>>
<jdoc:include type="modules" name="bottom_row_one_2" style="round_box" />
<div style="clear:both"></div>
</div>
</div>
<?php } ?>
<?php if($this->countModules('bottom_row_one_3')) { ?>
<div id="s5_bottom_row_one_3_mod" style="width:<?php echo $bot_row_one_3 ?>">
<div id="s5_bottom_row_one_3_inner_mod"<?php if($this->countModules('bottom_row_one_4')) { ?> style="padding-right:14px"<?php } ?>>
<jdoc:include type="modules" name="bottom_row_one_3" style="round_box" />
<div style="clear:both"></div>
</div>
</div>
<?php } ?>
<?php if($this->countModules('bottom_row_one_4')) { ?>
<div id="s5_bottom_row_one_4_mod" style="width:<?php echo $bot_row_one_4 ?>">
<div id="s5_bottom_row_one_4_inner_mod">
<jdoc:include type="modules" name="bottom_row_one_4" style="round_box" />
<div style="clear:both"></div>
</div>
</div>
<?php } ?>