^ could it have to do with the skip shift deal, I have heard that the mt82's have a thing built in where to save gas they will force you to shift from second to fourth. Does a light come on on the dash or anywhere when it happens? I know the 11's had this but I don't if they still do.
You should probably see your dealer to be on the safe side.

 

I think these trans do tend to grind a bit, even audible if you put sideways pressure on the shift lever when it is in gear. It really doesn't like anything but accurate shifts. That's why I try not to keep my hand closed on the shifter but just push it the right direction with an open hand. I use finger tips and the space between thumb and fore finger for shifts. This trans really schools you on proper technique

 

oh yeah your not the only one to feel that vibration/grind.I don't feel it through the shifter but through my left foot on the clutch pedal.It's not grinding but it feels like the syncros are still moving,using a gentle hand on the shifter helps plus slowing down your actual moving of the shift lever seemed to help.Timing of your shifting does help as well and other solutions I've read is changing the oil in the torque converter plus I've read somewhere that ford has a bulletin out that you should replace your clutch pedal assembly with one from a mustang shelby,cobra or 500 whatever the name is.I don't think you actually have to worry though your not grinding gears so to speak so no damage is being done.

 

There is a tsb on early build 2012 and 2011 models to change the transmission fluid. FYI there is no torque converter on a manual transmission, just on auto. From what I know the pedal replacement has to do with the clutch pedal sticking to the floor at high rpm.

 

my bad on the torque converter thing I don't know what the hell I was thinking,but I do feel the vibration but I'm not concerned about it as it seems a LOT of people feel that sensation.The only people I've seen that have had tranny problems are the ones that are either drag racing part time or maybe autocrossing but whatever they are really abusing the transmission,I'm 5000km into my new car and I've been a good boy but also I've been really bad and no issues so far.

 

Finally got my Barton shifter and bracket installed today and WOW, what a difference. In my 2013 I had no issues but with the Boss 302 if I revved any higher than 6000 rpm it wouldn't shift into 2nd and rarely would hit 3rd. Now it grabs all gears with no issue and feels so much nicer. I couldn't be happier and would highly recommend the upgrade.

 

I believe what manual GT owners and Shelby owners are doing is removing the clutch assist spring. It is supposed make the clutch part of shifting an improvement. See youtube etc.

 

Thanks for the input, and I am glad I am not the only one experiencing this. I have yet to beat the snot out of it, so I really haven't experience the 2nd to 3rd shift. It's disappointing that this is clearly a problem and Ford won't do anything about it. I guess that's business for ya.