<?php
/* current data being output to page

sizes : new Array(
    "Small -- 3\' 6\" (h) x 8\' 0\" (w) - 1 Panel",
    "Medium -- 4\' 0\" (h) x 9\' 1\" (w) - 3 Panel",
    "Mini -- 1\' 0\" (h) x 2\' 3\" (w) - 1 Panel",
    "Mini -- 1\' 0\" (h) x 2\' 3\" (w) - 1 Panel",
    "Mini -- 1\' 0\" (h) x 2\' 3\" (w) - 1 Panel",
    ""
),

sqFeet : new Array(
    28,
    36,
    "6",
    "6",
    "6",
    0
),

Sizes input values:
mini: 5
small: 0
medium: 1
large: 2
custom: 3
*/

your code:

 sizes : new Array(<?php
 $sku = $_product->getSku();
        echo ($_product->getSmallSize() && $_product->getSmallSqft()) ? '"'.addslashes($_product->getSmallSize()).'",':'';
        echo ($_product->getMediumSize() && $_product->getSmallSqft()) ? '"'.addslashes($_product->getMediumSize()).'",':'';
        echo ($_product->getLargeSize() && $_product->getSmallSqft()) ? '"'.addslashes($_product->getLargeSize()).'",':'';
if (substr($sku,0,3) == "DPC") {
        echo ($_product->getMiniSize() && $_product->getSmallSqft()) ? '"'.addslashes($_product->getMiniSize()).'",':'';
        echo ($_product->getMiniSize() && $_product->getSmallSqft()) ? '"'.addslashes($_product->getMiniSize()).'",':'';
        echo ($_product->getMiniSize() && $_product->getSmallSqft()) ? '"'.addslashes($_product->getMiniSize()).'",':'';
}
?>""),

 sqFeet : new Array(<?php
        echo ($_product->getSmallSize() && $_product->getSmallSqft()) ? addslashes($_product->getSmallSqft()).',':'';
        echo ($_product->getMediumSize() && $_product->getSmallSqft()) ? addslashes($_product->getMedSqft()).',':'';
        echo ($_product->getLargeSize() && $_product->getSmallSqft()) ? addslashes($_product->getLargeSqft()).',':'';
if (substr($sku,0,3) == "DPC") {
        echo ($_product->getMiniSize() && $_product->getSmallSqft()) ? '"'.addslashes($_product->getMiniSqft()).'",':'';
        echo ($_product->getMiniSize() && $_product->getSmallSqft()) ? '"'.addslashes($_product->getMiniSqft()).'",':'';
        echo ($_product->getMiniSize() && $_product->getSmallSqft()) ? '"'.addslashes($_product->getMiniSqft()).'",':'';
}
?>0),


now I see another problem, what if there is no small size or medium size.. you will have the same problem.

why don't you just do this:
also, there is no reason to check for DPC on this, what if they decide to have mini in other skus.
this will output a value or 0 for each possible size.
also, the mini or other sizes won't show because you are only showing available ones as inputs.
another thing, no reason to do the check you were doing the if product size and product sqft
this is cleaner and makes more sense, and you don't need to duplicate dummy data.

sizes : new Array(
<?php
    $sku = $_product->getSku();
    echo !empty($product->getSmallSize()) || $product->getSmallSize() != "" ? '"'.$product->getSmallSize().'", ' : '"", ';
    echo !empty($product->getMediumSize()) || $product->getMediumSize() != "" ? '"'.$product->getMediumSize().'", ' : '"", ';
    echo !empty($product->getLargeSize()) || $product->getLargeSize() != "" ? '"'.$product->getLargeSize().'", ' : '"", ';
?>
    "", // this is the one for custom
    "", // this is a blank one because you don't have a value of 4
<?php
    echo !empty($product->getMiniSize()) || $product->getMiniSize() != "" ? '"'.$product->getMiniSize().'", ' : '"", ';
?>
    ""), // this would be for value 6 but there isn't one anyway

sqFeet : new Array(
<?php
    echo !empty($product->getSmallSqft()) || $product->getSmallSqft() != "" ? '"'.$product->getSmallSqft().'", ' : '0, ';
    echo !empty($product->getMediumSqft()) || $product->getMediumSqft() != "" ? '"'.$product->getMediumSqft().'", ' : '0, ';
    echo !empty($product->getLargeSqft()) || $product->getLargeSqft() != "" ? '"'.$product->getLargeSqft().'", ' : '0, ';
?>
    0, // this is the one for custom
    0, // again an empty one because no value of 4
<?php
    echo !empty($product->getMiniSqft()) || $product->getMiniSqft() != "" ? '"'.$product->getMiniSqft().'", ' : '0, ';
?>
    0),