Unroot Android (remove symlinks by Link2SD)

Before posting this, I tried looking at other forum threads and over the internet in the last week, but could not find a solution so far.

I have a Huawei Y300 with Android 4.1.1. It was rooted and was pretty much fine except for some issues (they happened in time, are not caused by the rooting itself). Meanwhile, I changed the SD card and the defects include:
- cannot set contact photos (it stops when it tries to crop image)
- cannot change theme (it shows it empty and says "internal storage full" - which is not true, plenty of free space shows up in app manager)
- can't use file manager - doesn't see anything from Local
- without a card in it, gallery and camera don't work at all

I did a factory reset and cleaned the davlik folder, but didn't change anything.

The problems come, I think, because Link2SD creates symbolic links to some folders, and those folders are not the same in a new card. For instance, when I use Root Browser and click Properties on some folders, I get:
Path: /sdcard

But, when I use phone's File Manager, it does not see the files from "storage0", it shows only files located in "storage/sdcard1"

I tried to do a system update, by putting a firmware zip (or app) on the card. But it does not see it there, because it sees what the symlink tells it to see. So I'm stuck in a loop.

Because it was impossible to make Link2SD see the new card, I used another phone, with Android 4.4. After endless attempts, I got that phone to see the two partitions on the card and function. (I had to make Link2SD system app and chose ext4 for second partition.)

I took the card back to the problem phone and only sees the first partition, not the ext4 one.
In Link2SD storage info it shows:
Internal (69% free)
SD Card (unmounted)
External SD (93% free)
Second Partition (not found)
System (33% free)

When I click Recreate mounting script - it says sd card not found.
Relink files: /data/sdtext2 not found

I basically would like to get the folder structure back to the original settings, maybe use the phone without card or with a new card, with or without rooting - just the simplest way possible, but to be able to use photos for contacts and wallpapers.

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