Yes, a considerable difference. The 289 cobra has a flat lower lip on the radiator opening resembling the letter D with the flat side down. It also has almost vertical sides with very small and flat wheel flares...it is typically referred to as a slabside (a good mental image). The front suspension is a transversely mounted leaf spring. I believe it also has a narrower track width, but I am not 100% certain off the top of my head. The 260/289 cars were based on the AC Ace.

The made very few FIA cars (3 or 6 or so?) to qualify in FIA races. They were 289 cars with much larger wheel flares, 2 distinctive creases in the fender - they supposedly had to fit a certain size suitcase in the trunk and just slammed it shut and it dented the aluminum trunk lid. I am sure there are a few other differences (maybe dash layout?) that I am not sure about.

For the 427 cars, they built a whole new tube frame for the bigger/more powerful engine and fitted a wider body with bigger flares and 4 wheel independent suspension.

I am sure I missed a lot of things, but that is a start.

 

The bodies are vastly different. The 289 was the original body style. There are four styles to the 289 configuration - slabside, comp, USRRC, and FIA. The slabside is narrow and flat fender flares. It was fitted with a 260 V8 and then a 289. Wheels were wire spokes and deflected considerably during racing. Slabside exhaust was undercar and exited out the back

Comp body styles are large fender flares added front and rear for wider tires. Doors were unchanged. Wheels were the five spoke FIA wheels. Exhaust is sidepipes that were down low and slightly under the rocker panels. They exited in front of the rear tires

FIA body styles had wider rear hips to accommodate wider wheels and tires. FIA wheels were used on these cars. Because of the wider hips and flares, the doors are "cutback" in order to make room for the wider wheel openings.

The USRRC is the other style. it had a tiny plexiglass windshield. Maybe some other changes I'm unaware of.

There are numerous other differences, like the radiator opening, taillights, trunk pan, and roll bar and fuel tank placement and sidepipes on the 427, which were moved up for additional ground clearance. They come out from a notch in the front fender.

On the 289 cars, the fuel tank is located right behind the cockpit, hence the filler on the rear deck lid. Comp cars (FIA, Comp and USRRC) had a splash guard around the filler to prevent gas spills on the driver. The roll bar is forward braced because the gas tank location prevented the brace from going towards the rear. On the 427 cars, the tank was relocated underneath, the roll bar brace changed, and the filler relocated to the hip.

Throttle pedals are different as well as the footboxes. The footboxes on the 427 cars are more narrow in order to fit the 427 FE engine.

There are still more but I'm tired of typing

 

Thanks for asking the question and for those that answered. I have wondered the same myself. Carl

 

Rich and Bill are pretty much on.

There were only 5 289FIA's ever build only 3 exist today. Even a white one raced on the Targa Florio. The White one had wider flares.
To be legal for the FIA races, the cars need to be street legal and registered in the homeland of the race team. Shelby did not like the idea to have a speedometer in the car - so he moved the gauge all the way to the right. One signature of the 289FIA.
Another signature of that car are the dimples on the trunk lid. Also a FIA regulation, a specific size of "luggage" needed to be fit in the car. Well, as the first inspections rolled around the box did not fit. The mechanics had to take the lids off and drive the dimples. There were only 3 289FIA's done that way, how Shelby got away with the other two is lost in time.

 

Just a little side note, it was the 289 race car which made Carroll Shelby famous for winning races...

 

This may be blasphemy on this site but go to the 4 min. mark and they go over some of the differences and history.

 

Two FIA pictures...

here the CSX 2301 1964 in Germany

the CSX2345 (#176) and CSX2260 (#177) and CSX2301 (#175) at the Sierre-Montagna race in Aug 1964

And the famous Carroll Shelby, with flag, and Ken Miles celebrate a victory at Mid-Ohio in a 1963 factory Cobra race car CSX2129.