It looks like I was right and the exhaust was causing excessive back pressure. Took the car to a Powerflow dealer at the weekend and had the twin outlet back box taken off and replaced by a single outlet.
As soon as I drove off down the road the difference was amazing. Where as before you'd accelerate and you get power,slump,power,slump - it was more power,power,power. All I need now is a pre-cat and I think the exhaust route will be done with.