Stuart.
While it is possible the water is rain coming in through the heater if its drain hole is blocked, or the heater matrix is leaking engine coolant into the cabin, or the windscreen sealant has perished, the obvious candidate has got to be the rag top.
The fabric may be intact, but it must have some sort of seal around the edge which may have been damaged. I have never dealt with a soft roof so I can not be any more specific. You also said cleaning the drainage channels helped, so if they are accessible can you test each one by pouring a little water through them to see if they really are clear?