Thought I'd give a update on how things went.
Got a custom exhaust made up which is 3" to the y-piece then 2.5" to the exits with the 3" downpipe and sports cat. I'm still not sure if it's running as it should, it hasn't got the surge of power I was expecting unfortunately. I had to revert it back to standard before I got all the bits fitted to test out the new map so was running it standard the week before I fitted the exhaust and injectors, this ment I couldn't compare the stage 1 to stage 3. I honestly feel like it's slower than stage 1 now and the only thing that could be causing it is the custom exhaust having less back pressure than the one that BSR specify and it's loosing power.
As the revs climb it feels like it's really struggling to pull and losing some horsepower as stage 1 would bounce of the redline without any troubles and the torque lower down tales off very early compared to before. This is just my thoughts and aren't great as I couldn't have a direct comparison one after the other.
At some point I'm going to try and get to a friends who has this setup, but with the 2.5" exhaust and then I'll know for sure.
The one good thing is that it sounds very nice, but I'll need to get a centre box for the 400mile trip home as it's drones once you get above a certain speed, dunno..