Theirs a couple things it can be that's causing the water leak.
First thing check the drains, tip water into these on each side, your be able to see little holes towards the front of the frame on each side. The water should drain an come out by the front wheels.
If the drains seem all ok, I'd probably say its going to be the seal between the frame and the roof. What we usually do is remove the frame, remove the old perished seal and then bond the frame down with mastic. That will all most definitely solve it.
I do these for £50
Saying all that though, if you removed a clip and now it's started surely that's your first port of call.