not sure exactly what you mean but...
if the two pipe flange is sat on the bench the centre of the start of the 2.5" section (the Y piece) is 200mm, so add on the 25mm and the total height is 225mm where the 2.5" starts.
I know the flange is 10mm, the flexy is 100mm and the 90 degree bend is 125mm which should make 235mm, but it's 225mm as the Y piece angles slightly to give clearance for the undertrays.
You should weld the flexies straight to the flange, then with 'trial and error' tack weld and double check the section as you go along, it's not a part I would make off the car, you really do need to be trial fitting as you go along :thumbup: