I'm pretty sure I have figured it out guys. Thanks to everyone who posted in this forum giving me the clues that were needed to put this to rest. So the code is as follows:
line: 2179 var fileNameBody = fileNamePrefix;
//fileNameBody += "" + zeroSuppress(i, 4);
//fileNameBody += "" + layerName;
fileNameBody += layerName;
What this does is get rid of the prefix for most layer names. The issue that many of us had after was that when layers were in groups, it still had a prefix when saved. To fix that you need to alter one more line of code:
line: 2219 //fileNameBody += "_" + zeroSuppress(i, 4) + "s";
Essentially you need to comment out this code, which should be under the "var fileNameBody = fileNamePrefix;" line of code. This should remove the prefix even if your layers are grouped.
The only code you need to change is what I have coded to be red.
Disclaimer: line number in code may vary by what version of photoshop you have. You can get around this by simply using your applications search feature to search for the code. Make sure you remove the "//" or else it won't find what you are looking for in the code.
I hope I help someone with this.