How can I start a loop at a specific number?
You definitely don't need JS here.

I'm  a bit pushed for time, so this won't be an epic answer, but e.g. with your select, you should not be using a hidden field for the qty.  

The select itself just sets the quantity value - either 1 if the option is chosen or no value if the option is not chosen....it really is as simple as:

&lt;form&gt;

  {# primary item - use whatever input you like for qty, or just do it in a hidden... #}
  &lt;input type="hidden" name="items[9999][purchasableId" value="{{ mainproduct.purchasableId }}"&gt;
  &lt;input type="hidden" name="items[9999][qty]" value="1"&gt;

  {# accessories #}
  {% for accessory in accessories %}
    &lt;input type="hidden" name="items[loop.index][puchasableId]" value=="{{ accessory.purchasableId }}"
    &lt;select name="items[loop.index][qty]"&gt;
      &lt;option value="1"&gt;Yes Please&lt;/option&gt;
      &lt;option value="0"&gt;No Thanks&lt;/option&gt;
    &lt;/select&gt; 
  {% endfor %}

&lt;/form&gt;


This will cause the following to be posted - 
items[0][purchasableId] = 45 

and depending on the user choice, either 

items[0][qty] = 1 or items[0][qty] = 0

...and multiAdd will just ignore this if the qty = 0.

The key thing to understand is the value of the index is totally irrelevant as long as it is the same for the purchasableId and the qty - it just acts to join the data together - you could literally send:

items['TrumpIsInsane'][purchasableId] = 45
items['TrumpIsInsane'][qty] = 1


...and it should still work.  So for the primary product I just use something like 9999 so that I am sure it won't conflict with any of the loop indexes (I'm not going to have 10000 accessories eh?) -> it's just a made up number.

For completeness, radios would only be slightly different:

&lt;form&gt;

  {# primary item - use whatever input you like for qty, or just do it in a hidden... #}
  &lt;input type="hidden" name="items[9999][purchasableId" value="{{ mainproduct.purchasableId }}"&gt;
  &lt;input type="hidden" name="items[9999][qty]" value="1"&gt;

  {# accessories #}
  {% for accessory in accessories %}
    &lt;input type="hidden" name="items[loop.index][puchasableId]" value=="{{ accessory.purchasableId }}"
    &lt;input type="radio" name="items[loop.index][qty]" value="1" checked&gt; Yes Please&lt;br&gt;
    &lt;input type="radio" name="items[loop.index][qty]" value=""&gt; No Thanks&lt;br&gt;
  {% endfor %}
&lt;/form&gt;