Okay chaps, I've just had a good chat with Steve at the factory and as always he has been very helpful.
He said he believes it will be one of two things: -
1) The seal around the wiper wheel box spindles - basically where the wiper spindles poke through the body is a very tight fit. Morgan fit a seal and then waxoyl around the seal. It is worth checking whether these points are still sealed and if not, applying some waxoyl as if they have dried out, water could seap through.
2) The heater drain hose has come loose - if you lay across the seats and look toward the gearbox cover, there should be a small pipe that goes from the back of the heater through the bulkhead (by the gear box cover). The pipe should be attached to the back of the heater (the heater has a 'stub' pipe on the back of it), this allows again moisture to drain.
This can come loose and could cause some water ingress; however, it was stressed that this would generally be the cause of water on the carpet, not the transmission tunnel.
I hope this helps

(and again, a big thank you to Steve at MMC)
Simon