Sorry to hear about the water problem but glad to hear the clearing of the tube fixed things up.
Our Focus has no gap in the rubber seal. It looks like it is glued together. Maybe the glued seam came apart on your car? If you're not the first owner then perhaps the previous owner replaced the seal?
Is the roof centered in the opening? It looks like there is quite a gap at the back.
Snorkel delete, K&N filter; FSWerks RMM insert, JBR rear sway bar, 63 mm throttlebody, MST intake tube, Borla Touring cat-back, FocusPower tune.