Thank you for your response nicolas. We managed to get the plug-in at least showing during the checkout process. It turns out that the response handler on the fedex.php file is only conditioned to react to "HighestSeverity" values of "ERROR" and "SUCCESS" when dealing with the response string. But there is another possible value for the "HighestSeverity" variable which is "WARNING" which was what we were getting, so since there was no condition to deal with this value it did not do anything past that point and it is why it was not showing up. Just a quick mod to the "SUCCES" conditional and finally it showed up:
This is the change we made to the conditional expression on line 803 of the fedex.php file:
if($response->HighestSeverity == "SUCCESS" or $response->HighestSeverity == "WARNING")
We have not tested it through yet, but I am guessing we are still going to run into the same issues as everyone else here so we will probably need to buy kasseyhadi solution, but at least we know it will end up working. Our main concern was that it was not showing up at all.