is there a difference between the 98 cobra timing chain cover and the 99 timing chain cover?

 

Yes. The 98 has diff bolt patterns for the coil pack brackets and I believe they have a different idler arm location, but that's not a big deal at all. Your main concern should be that they have the same bolt holes for the heads and I believe they do. I think you can put a 96-98 cover on a 99+ but not the other way around because of the accessories that the 96-98's have. The gt's are def different as far as bolt holes(size). I think you should be fine.