Bad Topology got after applying modifier I have somewhat a bad topology on a model I made and it messes up with the shading and the material itself, it is a lot of edges that are intersecting with each other and I am not sure on how correctly I should fix this problem, I know how to fix it manually though. Do you have any recommendations that could make this go faster than just doing it manually?
Here are screen captures of my viewport  : 


Before I got the model, I applied a subsurface modifier and an array modifier with object offset, with a simple deform modifier on this model I don't know if my original topology was bad or not
Your topology looks decent.
I'm pretty sure your array modifier didn't match start and end 100%. That created an overlap which you see in your 1. screenshot. Repairing this is tedious, it would be much simpler to go back to before you applied the array and fixing it in the base shape. If you use a segment of a circle or a sphere and then rebuild the circle/sphere from the modified segment with a circular array, make sure not to touch the outermost vertices, as they have to align perfectly in the end.