Anders, this crack is hidden under the belt line. The glass liminate is bubbling. I would remove and replace the glass by using propane heat, re-align the vent window frame and weld the crack. It looks like this crack was caused by pulling the door shut by using the window frame instead of pulling the inner door handle.
Penetration is the key to a successful weld. The crack needs to be ground to a 'vee' on both sides, then welded using mild steel. In places like this, I like to 'lap weld' a slightly larger piece of steel over the newly welded crack. This spreads the stress away from the weld and it makes the area thicker.
Although not 'pure stock', you can buy tempered glass which is solid, but the same thickness as your original glass. New cars use tempored glass. Being solid, it cannot bubble and comes in clear or a few tint colors.
I suggest you pull your engine before painting. I pull my engine and trans together, but you can do it separately. To me, the engine is much easier to marry outside the vehicle.
To prepare, pull the hood off and set it aside. Hoist your car off the suspension with solid jack stands holding up the frame members in all four corners. Before getting under the car, give it a good shake to make sure it is stable.
Use equipment that is quality and substantial because your life depends on it. I would NOT try pulling the engine by myself. If anything goes wrong you want help to be near. This work has been safely done millions of times. There is no reason why anyone should take unnecessary chances. Be safe so we can enjoy our hobby together, Anders. - Dave