Drain holes from above with the roof removed
Whatever you do, don’t push too hard, or you’ll disconnect the tube from the tray. If this happens there’s a lot of work involved in dismantling the area behind the seat to get at it.
Try finding the bottom of the drain tube and pushing something up from the bottom, I find a piece of old flexible net curtain rod is the best.
There is a sort of ‘flappy thing’ at the bottom of the tube, it’s designed to keep noise from getting up the tube and into the car, but it can allow bits of debris to get stuck.
Drain holes in the sills 
A view of the drain holes shot through the rear [unzipped[ window
