Starting at the nose, the earlier Spitfire would have a 3-bladed prop and a differently shaped nose cone. The Mk.IX had to have the fuselage extend to accommodate the more powerful engine, and also the shape here was more beefier.
Due to the differing wing armaments, there is some differences in panel lines/access doors and you will need to add an additional ejector chute on each wing. There should also be gun bay vents located outermost on the underside of both wings. There is a bulge on the wing top located above each wheel well to accommodate the landing gear when in the up position. The central scoop underneath the belly was smaller/narrower, and ailerons were fabric covered.
The canopy would be narrower, and on the port side there was an oval section. Antenna masts might be different (check references), but there would be a wire leading back to rudder, which also had a short mast.
Not sure if our combined lists are complete, but this what I arrive at off the top of my head.
regards,
Jack