Runs rough cant figure it out

I have a 90 xj 4.0, About a month ago i went and got an emissions test and failed, the guy there said a tune up should fix it, so i went and changed plugs, wires, oil/ filter/ air filter, fuel filter, transmission fluid. took the throttle body off replaced the gasket and cleaned it. There right after that my fuel pump would always be on as soon as the battery was hooked up and would eventually drain my battery if it sat, but as of right now i keep it unplugged when im not working with it but, it runs really rough it sounds like its missing i then replaced all the plugs again with better spark plugs and still the same thing sounds like its missing, any ideas or anything would help thank you

and i also took off my cat thinking it was clogged and its is still running the same way and one other thing i just read on another forum, be hit me, is theres a real good chance i may have got one of the spark plug wires mixed up so would any body have a diagram or the correct order