This will probably be a little messy. Throughout this thread the code has changed a bit and I've done my work on several computers (so I was updating an older version that was on this PC). Also, the biggest thing I didn't want to deal with was the HTML/formatting of this form. So with that aside, understand this code works, but cannot be directly copied into your page as it'll likely break something. But if you're careful, you can take out the parts and place them as you see fit. As long as the core of this is on your page and the script is the same, it should work.

HTML Code:
Number of Items:
<select id="itemCount" name="itemCount" onchange="_ChangeItemCount(this)">
	<option value="1">1</option>
	<option value="2">2</option>
	<option value="3">3</option>
</select>
<br />
<br />
<p><input class="checkbox" value="withouttooling" checked="checked" name="tooling" type="radio"> No Tooling Design<br/><br />
<input class="checkbox" value="withtooling" name="tooling" type="radio"> With tooling design<br/><br />
<small style="FONT: 10px Arial,Helvetica,sans-serif">(All tooling Gold unless otherwise specified)</small></p>
<p>Tooling design inset<br/><br />
Choose<br />
<input class="checkbox" value="1/2 inch" name="inset" type="radio"> 1/2”<br />
<input class="checkbox" value="3/4 inch" name="inset" type="radio"> 3/4”<br />
<input class="checkbox" value="1 inch" name="inset" type="radio"> 1”</p>
<p>Plus $25.00 shipping</p>
<hr/>
<br />

<div id="itemDiv1">
	<strong>Item 1</strong>
	<br />
	Width<br />
	<input class="short" onchange="Calculate(1)" name="width1"><small>(in)</small>
	<br/><br />
	Length<br />
	<input class="short" onchange="Calculate(1)" name="length1"><small>(in)</small>
	<p style="PADDING-BOTTOM: 0pt"><strong>Total Cost</strong><input class="short" onfocus="this.form.elements[0].focus()" name="totalcost1" id="totalcost1" /></p>
</div>


<div id="itemDiv2">
	<strong>Item 2</strong>
	<br />
	Width<br />
	<input class="short" type="text" name="width2" onchange="Calculate(2)" /><small>(in)</small>
	<br /><br />
	Length<br />
	<input class="short" type="text" name="length2" onchange="Calculate(2)" /><small>(in)</small>
	<p style="PADDING-BOTTOM: 0pt"><strong>Total Cost</strong><input class="short" onfocus="this.form.elements[0].focus()" name="totalcost2" id="totalcost2" /></p>
</div>


<div id="itemDiv3">
	<strong>Item 3</strong>
	<br />
	Width<br />
	<input class="short" type="text" name="width3" onchange="Calculate(3)" /><small>(in)</small>
	<br /><br />
	Length<br />
	<input class="short" type="text" name="length3" onchange="Calculate(3)" /><small>(in)</small>
	<p style="PADDING-BOTTOM: 0pt"><strong>Total Cost</strong><input class="short" onfocus="this.form.elements[0].focus()" name="totalcost3" id="totalcost3" /></p>
</div>


<br />
<br />

Grand Total: <span id="grandTotal"></span>

<script>
if(typeof(_N) != "function") function _N($n, $d) { return ($d) ? Number($n).toFixed($d).toString().replace(/\B(?=(\d{3})+(?!\d))/g, ",") : $n.toString().replace(/\B(?=(\d{3})+(?!\d))/g, ","); }

$itemCount = 1;

function _ChangeItemCount($a) {
	$itemCount = $a.value;
	document.getElementById("itemDiv1").style.display = "none";
	document.getElementById("itemDiv2").style.display = "none";
	document.getElementById("itemDiv3").style.display = "none";
	for(var $i = 0; $i < $itemCount; $i++) {
		document.getElementById("itemDiv"+($i+1)).style.display = "block";
	}
	_CalculateTotal();
}
_ChangeItemCount(document.getElementById("itemCount"));

function Calculate($a) {
	var order_total, length, width, i;
	order_total = 0;

	length = parseFloat(document.forms[1]["length"+$a].value);
	width = parseFloat(document.forms[1]["width"+$a].value);

	if(length > 0 && width > 0) {
		order_total = length * width;
		for(i = 0; i < document.forms[1]["tooling"].length; i++) {
			if (document.forms[1]["tooling"][i].value === "withouttooling" && document.forms[1]["tooling"][i].checked === true) order_total = order_total * ".30";
			if (document.forms[1]["tooling"][i].value === "withtooling" && document.forms[1]["tooling"][i].checked === true) order_total = order_total * ".40";
		}
		order_total = order_total + 25;
	} else {
		order_total = 0;
	}


	document.forms[1]["totalcost"+$a].value = '$' + _N(order_total, 2);
	_CalculateTotal();
}

function _CalculateTotal() {
	var $grandTotal = 0;
	var $f = document.forms[1];
	for(var $i = 0; $i < $itemCount; $i++) {
		var $tmpTotal = parseFloat($f["totalcost"+($i+1)].value.replace(/[^0-9.]/g, ""));
		$grandTotal = (isNaN($tmpTotal)) ? ($grandTotal) + 0 : ($grandTotal) + $tmpTotal;
	}
	document.getElementById("grandTotal").innerHTML = _N($grandTotal, 2);
}
</script>
This is pretty simple overall, but to explain (so you know what you're getting and what to expect), this has a dropdown/select element at the top. When you change this, a new function will show/hide the number items (currently set at a max of 3). Each 'item' display includes a width, length and totalcost field. Each of these items functions independently, with their own values and prices. The tooling and options are at the top, but not part of any specific item (so the value is applied to all items). The grand total calculates the total based on which items are currently visible/available.

Again, be careful when adding this code. I didn't copy your entire form so the actual HTML part needs to be inserted as you feel it should be placed on your form. The javascript can be copied directly with no issues.