With the help of a colleague we figured out a way to do this. Here's for anyone trying to do something similar.
First here's the script we came up with:
oldFrame = $('#mapframe');
newSrc = $(this).attr('href');
newFrame = $('<iframe>').attr('src',newSrc).attr('id','mapframe').attr('width','597').attr('height','602').appendTo('#map .map');
1 - Make sure this follows other script files/libraries that are loaded on the page.
Here is an example of a link that replaces the batchgeo map in the iframe with a google map of the dealership link.
<a href="https://maps.google.com/maps?q=1151+Hartford+Turnpike+++++++Waterford,++CT++06385&oe=utf-8&client=firefox-a&hnear=1151+Hartford+Turnpike,+Waterford,+New+London,+Connecticut+06370&gl=us&t=m&ie=UTF8&hq=&z=14&ll=41.4077,-72.183221&output=embed" class="changeMap"><strong>Bob's Farm Supply</strong></a>
Two keys with the link.
1 - a class is added so the script finds and uses those <a> to change. class="changeMap"
2 - the href needs to be the src found in the "Paste HTML to embed in website" iframe code from google maps. The key is the "output=embed" at the end of the url used in the embed version, which is not found in the short link or long url...
Finally, the iframe that's being used as the stage to show all these changing links needs to have an id for the script to use.
<iframe name="mapframe" id="mapframe" src="http://batchgeo.com/map/c3eb1a85588c20553c99bcdb05b756f7">
Hope that helps