I stripped the gun down and noticed sometimes the spent shells wont extract. It seems as if the ejector/bolt stop arent fully engaging the casing.

The video can be slowed down with this link (controls are under the video) - slow down to 1/4 speed and its more visible. The jam occurs at the end of the video
http://www.youtubeslow.com/watch?v=8YW6TLdclPg

What is your ammo?  Have you replaced the gas meter bushing or is it the factory one ?

Ive tried a few different ammo: XM193 and fiocci mostly. Its pretty consistently jamming once or twice every 10 rounds.

Havent replaced anything but the stock (sitting in the factory folder). Rifle is brand new aside from that.

It looks like it's cycling slowly. My mini's ejection is crisp and forceful, in the video, it looks cumbersome.
Perhaps the ops rod is rubbing on the upper hand guard? Have you tried removing the upper guard and cycling it? Might be binding somewhere.

I'm really not all that familiar with Mini-14s but is it properly lubed?  Garands and M14s like grease instead of oil or CLP.

<double tapped>  l must be over lubed.  

On the 187 series and later Mini-14s and Ranch Rifles, the bolt stop serves as the ejector, replacing the ejector spring and plunger found on the earlier series.

There are a few possible issues:

1) Be sure the recoil spring guide is placed so that the long side is between the pin and barrel.

2) Check to make sure the ejector on the bolt stop isn't broken and still extends all the way into the slot in the bolt.

3) If you are using a shock buffer, it may be slightly too thick, reducing the slide over run distance just a bit too much.

4) It may be under gassed.  If you're using the original gas bushing, there could be an obstruction in either the gas port or the gas bushing.

5) It's not an AR-15, it likes to be run wet (for that matter so does the AR-15).   Garands, M1As, M1 Carbines and Mini-14s all run well if you wipe a light coat of oil on everything and then grease the shiny spots on the bolt and slide, and also the bolt lug and bolt lug recess in the slide with a gun grease - Rig, Tetra Gun Grease and surplus Military Rifle Grease all work well.