You may be able to make your problem easier by reducing the number of quads that you have to deal with.
You know that some of the quads form a closed shell. Therefore, those quads are connected at their edges. If three mutually adjacent edges of a quad (that is, the edges form a closed loop) overlap the edge of another quad, then these quads might be part of the shell (these mutually adjacent edges serve as the boundary of a 2D region; let's call that region the "connected face" of the quad). Make a list of these "shell candidates". Now, look through this list and throw out any candidate who has an edge that does not overlap with another candidate (that is, the edge overlaps an edge of a quad that is not in the list). Repeat this culling process until you are no longer able to remove any quads. What you have left should be your shell. Create a "non-shell quads" list containing all of the quads not in the "shell" list.
Draw a bounding box (or sphere, ellipse, etc) around this shell. Now, look through your list of non-shell quads, and throw out any quads that lie outside of the bounding region. These are definitely not in the interior.
Take the remaining non-shell quads. These may or may not be in the interior of the shape. For each of these quads, draw lines perpendicular to the quad from the center of each face that end on the surface of the bounding shape. Trace each line and count how many times the line crosses through the "connected face" of a quad in your shell list. If this number is odd, then that vertex lies in the interior of the shape. If it is even, the vertex is on the exterior. You can determine whether a quad is inside or outside based on whether its vertices are inside or outside.