Also, have you double checked the camshaft timing using the special cam tool with the flywheel locked?

 

I've replaced the MAF sensor and I've done a leak down check on the intake and there are no leaks.

 

Yep, I have the BMW cam locking tool and I have checked it 3 different times over the 3 months I've been working on this.

 

I just did a cylinder leak down test to make sure nothing is leaking from the valves or pistons and in the process of doing that I heard a click come from the piston on cylinder 1 and cylinder 4 when i had it at 20 psi. Which makes me think the piston might be rocking back and forth. The click noise from the piston will only happen once, in order for it to happen again I have to rotate the piston up and down a little bit then the click will happen again. From my experience I think the rods wrist pin bearing might to too lose and letting the piston rock in the cylinder. In any case here are the leak down results if your curious.

Cylinder 1: 93psi/100psi
Cylinder 2: 98psi/100psi
Cylinder 3: 97psi/100psi
Cylinder 4: 92psi/100psi

 

Click noise could potentially point to a hydraulic lifter issue.