Clicking transmission/axle?

[zholtz]

109k miles, Honda Civic 2012 LX.
So here is the problem in a video then a description of the problem below
https://youtu.be/_yeJ24UlKRQ

So I’ve been having some issues and getting some shaking on acceleration so I fixed all engine mounts and a new drivers side cv axle. I was going to replace the passenger side when I found this.
If I jack up the front two tires off the ground, and spin them there is this clicking sound where the axles meet inside the transmission. NOT where the inner cv joints are but more like where they meet.
The tires are reacting to the change in speed and make a clicking noise. Please help. I have even heard that same noise when pressing the accelerator and picking up my speed.
My transmission has had no issues.