Is there any engine or computer differences between an auto or manual trans car. Traction controls, horsepower ratings etc.... Ifound a 98 Z28/auto car that looks fairly cleanwith a bunch or mods that I can probably get for 5k.

 

The computer knows that it has an Auto and it knows that it needs to tell it when to shift, other than that you're looking at the same car. If the car is a good price go for it, although you have to watch out for cars that have been heavily modded because it's likely that they've had the crap driven out of them.