Knocking/vibration through shifter (lots of details)

A long stethoscope is not a bad idea. I think the Alinement Shop has microphones now for clunks an noise detection.

 
I took it to a trans shop and they said that everything looks good. I do have a new clutch and this T5 was rebuilt about 40k miles ago. It drove just fine in the air
 
I suspect you are on the right trail with a bearing or something in the transmission if it does this under load and not downhill.
If the tail shaft and yoke are really fine, closely inspect the U joints and hope at least one is dry, heat discolored or has a frozen cap. The next answers cost more.
 
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Well, I stopped by a driveshaft place because it was so close to my job. The guy said everything looked good. They didn’t balance it but they figured it was ok since it was still marked “balanced” and the joints looked new. However, another guy noticed that the transmission sits a little too much to the passenger side. I’ve always mentioned the position of the trans whenever I enquired about my issue but I’ve been told numerous times that it sits just fine so I left it out, this time. Anywho! He pushed it a little to the left side with a pry bar and it sounded like it may have made a difference. I’m not for certain until I can loosen the motor and trans mount to try and reposition the transmission. I’ll try that this weekend.
 
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All mounts are new and I can’t tell if the motor is leaning. However, the previous owner said he did something to motor mounts to help it sit lower. I think he said he installed fox mounts but they should be the same. I think.