Need to delete junk/system files/crap/ from installing custom rom but keep root topic

Hey all so I'm running 4.4.2 deodexed rooted with xposed, etc, etc. I went from rooted 4.1.2 to kitkat last month buy route of flashing deodexed 4.4 with partition flash and was able to keep root. Using Philz recovery ive always installed "clean to install new rom" but looking at the files and apps, etc now i have to much junk in internal memory/root of the sd card on my phone. I have a partitioned sd card. And basically ive flashed from backups. Tested and ran scripts, deleted scripts. Ive done alot so i need to delete the unused junk off my phone but not sure what to delete or what steps to use in Philz recovery. My main worry is loosing my supersu/root and messing up the partitioned sdcard. If i loose root on my phone the process of re rooting while on kitkat is extreme involving booting pc from a usb drive or cd and running virtual machine, etc etc. So i cant loose that. I do have backups on pc and 1 back up of my current rom on external sd card. I have Philz Recovery and link2sd.

Thanks
Josh