That will help.

ok 100% it is not the fly wheel. While it was making the noise I pulled the oil dipstick, and for the some reason the dipstick had a vacuum, and the noise immediately stopped. I put the dipstick back in for and let it run for a little while and the noise is back. I pull it and it disappears again. Some sort of crank case breather issue then? I'm so confused now.

PCV valve

My intake doesn't have an actual valve. It has a plate that says pcv on it and when I take that off there is a spring under it. ?

And under that spring is your PCV valve.

ah, sorry I feel kinda dumb now. So you think that is the problem? How does it come out once I pull the spring? Is it just sitting in there?

A needle nose pliers and it will come right out. If the O ring is gone it will make cause a vacuum in the crank case. Only other possibility is a bad gasket between the LIM and supercharger and it'* leaking from the intake to the PCV valve.

Even tho I swapped all my stuff onto this motor (oil filter bracket, oil pan, and the funnel inside the oil pan, intake and supercharger, and a bunch of the accessories, is there any way that the LIM would be different and could be causing this problem? They looked the same but I'm a bit of a hypochondriac when it comes to these things. The only reason I ask is because the reason I used my intake is because the one on the motor had the vacuum lines run a little differently as well as one of the plugs on the wiring harness.

I replaced the intake manifold gasket as well as the o rings when I swapped everything so the gasket can't be bad. Should there be oil when I pull that cover for the pcv valve? I coulda sworn there was oil on the spring.