I have deep pans on several trucks and all of them have a separate extension piece for the extra length so you can use the standard filter.
The dipstick reads the same regardless of the pans depth.A deep pan adds more fluid,but doesn't change the correct level needed to work.
The deep pan kits usually have a short tube or sleeve and longer screw to make up the difference in length.
If you are missing an o-ring,it will suck air because the o-ring is above the fuid level.
Mike.