I haven't got very far into my master series Spitfire, so I haven't got too much experience in this - but I too plan to tweak the design a little.
I want to put a transparent canopy on mine which will be cutting through a section of the spine. I plan to make a (slightly shorter) copy of the former that joins the tail section of the fuselage to the mid section, that will hold the spine, just aft of my canopy, in the way the original former does and hopefully have the same strength.
The challenge you have, is sussing out the shape of foam that wraps around the tail section. The template for mid section will provide a hint on the width of the foam piece at that end - but the curve will need to be a different shape in order to get the angle right.
Clipping the wings (if you're going for the low-altitude variant) and boxing out the bonnet for the griffon engine will be easier mods. Are you gonna give it a four-bladed prop?