3rd gear pedal down vibration

Hey guys, I am new to the Cobra world. I purchased a 2004 cobra convertible about a month ago. I knew it needed a few things because it sat for so long. there was a loud howl from the rear so I just had a shop rebuild the gears in the rear with stock 3.55 its perfect. super quiet. There was also a vibration coming from what felt like the rear before i had the gears done. I thought it could of been the rear end but it didnt fix it. it happens when you are in 3rd or 4th gear. when the rpms are on the lower side like 3000 and you give it hard throttle. it shakes pretty bad. i dont think its transmission because all the gears are super smooth going in. trans mounts, engine mounts, rear cradle bushings? has anyone experienced this before.
 
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