2013 Mustang Gt Sync Update Issues

I just tried to update the sync software on my car, I was unable to do so because the files couldn't be found on the USB drive. I followed the instructions to the letter from the Ford website on how to put the files on the USB drive and then upload it the car. Could the problem be that I have aftermarket performance software uploaded to the ECU along with an aftermarket air intake installed on the car? Any input would be greatly appreciated, Thanks!
 
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