Welcome to FTF, thought I wish it was under better circumstances for you
. You said you discussed the criminal record issues with someone. "there was missing criminal information on the original application which there was but had been talked about later on by the officer in charge of the firearms division
." You should see if you can get in touch with that officer. He may be able to help you explain the situation in terms that the police who have the problem will understand. Often when ordinary civilians try to communicate with the cops there is a misunderstanding due to different terminology.
The first officer seems to have evaluated your situation and decided that it really isn't a violation that should prevent your licensing. Perhaps he checked closer and found only a misdemeanor on your record whereas one of the immediate restrictions would be a felony conviction.
But, also consider that NJ is one of the most difficult states to get a concealed carry permit in. NJ does not recognize any other states license. NJ is "may issue", which means it's all up to the discretion of the judge who evaluates your application.