My understanding is that...
- 260 Cobras are considered MkIs
- 289 Cobras are considered MkIIs, and
- 427 Cobras are considered MkIIIs
The 260/289 Cobras were leaf sprung F/R and used 3-inch main chassis tubes. The 427 Cobras were coil spring and used 4-inch main chassis tubes. The MkIII chassis was completely re-engineered by Ford to handle the extra grunt of the big block motors.
No doubt there are many other differences, but those are probably the main ones.
AC Cars produced 289-powered MkIIIs (known as the AC 289 Sports, not Cobra) for the British and European markets, but these cars were not originally sold in North America.