Hi

I have same problem with sunroof not flush - no solution found yet.

Water leak in footwell:

I removed the footwell-sidepanel. There is a black plastic cover

about 4x5 inch. This cover on my car was not flush too and the water

leaks in there. It's a little difficult to remove, but possible.

I am planning to glue a 5x6 inch rubber piece over it.

This hole is according to some posts a ventilation inlet on Non-A/C cars.

I think the black plastic cover is slightly oversize and therefore don't fit. (After plastic injection molding the hot plastic part shrinks, which depends on the material but also on the molding-process parameters.)

Good luck