On my mini it was the sun roof and by the pollen filter. There is a button the changes the air circulation to just inside instead if drawing air from outside. Switch this to inside circulation, this will block water from coming in here, if no water after that, you found the culprit.
Well I've looked at the exhaust and to be honest the system looks huge anyway so will probably leave it for the moment. I think the whole system has been changed and not just the back box, which is good and will save a little money, for the moment anyway. Lol. What air intakes are the best to use. I know there are many different ones.
Best upgrade pound for pound (ive got the same car as you) will be an m50 inlet manifold conversion and big bore throttle bodies.costs about 500 quid to do and will give you 325 power :) Theres a guy in Chelmsford that does it,goes by the name of Alpina527,ive got all details when your ready :) I def getting mine done...soon as Ive sorted a few other bits 1st ;)