Another thing to check, how did you partition your sd card? Should be done with 4EXT recovery or gparted only (not minitool)
Backup and repartition your sd card if it's not done with those methods. One FAT32 partition, one 1.5-2GB max ext4 partition, no need for swap even though I think it says in OP.
To get around apps installing partially on sd card you could try a couple of things instead of replacing the script as it should work:
- Use titanium backup, long press an app and to move them to 'internal' to move to sd-ext, gets around having to navigate app settings
- I believe the ROM comes bundled with Xposed? Find a module called Modaco Toolkit, has a system option to 'Disable Forward Lock' which should prevent auto installation of apps to SD card (it works for me on Nexus devices preventing apps installing to virtual /mnt/asec sdcard partition, not tested with a real SD card but I believe the principle is the same, try it). If this method works, it's cleaner as apps should always get installed to 'internal' (sd-ext) in the first place.
Device: Nexus 5
| ROM: SlimKat
| Recovery: TWRP
Retired: HTC Desire
let's all try to get along ...but remember to search first...