Answer by user1208273 for Bash - Removing Linefeed character from a script

So after all that, turns out the real issue was I had just forgotten to append the folder to the file name so the reason zbarimg couldn't open the file had nothing to do with line feeds like I thought here is basically what fixed it:

zbarimg $folder/$ifile2

Thanks again to all those who offered help, sorry for the incompetence on my part may the blessing and forgiveness of the internet be upon me :)