Okay, let me summarize what you did:
1) You messed around with system apps.
2) You don't have a Nandroid-Backup - so you choose to factory reset your phone <- Which actually doesn't revert your modifications since the "system" partition remains untouched.
3) You set up your phone again but the system wizard keeps crashing.
4) You installed Apex Launcher and it fixed this problem.
5) Google Search isn't available after the factory reset, so you download it from Play Store and make it a system app.
6) Now your system feels slower in general.
--> Is that correct?
If yes, what exactly do you want to have now? Reset your phone like it was on the first day?
And why did you touch system apps at all? What did you want to modify?