I rooted my android 4.4.1 jellybean custom built smartphone so i could delete some malwares/adwares that installed themselves as system apps. Now i guess i got too "over-excited" deleting the malware/adware apps, that i mistakenly deleted a clean system app. Now my phone doesn't pass the boot stage and hangs after playing the intro animation. I hope you guys can help me since i didn't totally wipe off everything. Plus the phone is exactly like Google Nexus 5X.
To flash a new ROM, you need to install a Custom Recovery such as ClockWork Mod (CWM) or Team Win Recovery Project (TWRP). These are what will allow you to flash back to a stock ROM- which you said above was 4.4.1 jellybean. That is actually an issue, because jellybean is 4.3, and kitkat is 4.4.1. Just make sure you get the right one, and you should be good (just wanting to bring that to your attention!). I won't go through all of the details, but the gist of the process is: install your Custom Recovery first, then get the stock ROM onto your SD card (Plug into computer and drag/drop zip into phones internal storage). After that, boot into Recovery mode (which will launch the Custom Recovery you installed earlier) on your phone, find the zip and mount it. I won't go too in depth because there are some great articles that explain it way better than I could even try, but here's a start:
Flashing stock rom: http://lifehacker.com/how-to-flash-a-rom-to-your-android-phone-30885281