Ian, I had similar experiences, one really funny one was that water tended to gather in a pool around the door hinge area, occaisionally it would get whipped up by the wind, and spray straight in my face
Drain holes are a good idea, I also thought about panelling the front frame, and putting rubber strips to seal the front of the doors. Plenty other areas where sealing putty would help.
Importantly, check your main chassis rails by removing the sill securing screws that are underneath, if water runs out get some WD40 in there, and try to find where it is getting in.
Dave