Curtain Wall Panel Doors that are used in Curtain Systems applied to massing do not acquire a Level parameter. This will affect your ability to schedule doors according to Level. Their Level parameter will be blank in your schedule and this will place them at the top of your schedule.
This is one solution assuming that a door should/could be used in the Curtain System at all, meaning the wall is plumb and not a warped surface.
Switch the panel for the Empty System Panel (which leaves a "hole")
Sketch a plain curtain wall in the hole (no pattern, panel or mullion assignments)
Disallow Join for each end if desired (select curtain wall, right click over each blue grip "dot", choose Disallow Join)
Switch the panel for the curtain wall panel door you need.
Adjust height parameters of curtain wall.
This approach permits the door to acquire the level parameter. You can use the curtain wall panel door families you already have.
[Note: When using Linked Projects and scheduling those linked projects you can use Level to Sort/Group schedules. Unfortunately you cannot use Level as a Filter. You must come up with a different strategy for Filtering. The most obvious solution is to evaluate the door number (mark paramter) in some fashion.]