Can you run the Reparse Point Repair and then redo the Pre-Scan to see if it comes up clean then do a chkdsk /f to see what it makes of the files sfc /scannow was unable to repair.
To view the full chkdsk report, go into Event Viewer and when it has read the data, expand Windows Logs then click on the name Application/Action/Find and in the Find box type chkdsk or wininit and press enter.
Here it is:
Checking file system on C:
The type of the file system is NTFS.
A disk check has been scheduled.
Windows will now check the disk.
Stage 1: Examining basic file system structure ...
Cleaning up instance tags for file 0x6781.
Cleaning up instance tags for file 0x9ac03.
745728 file records processed. File verification completed.
10265 large file records processed. 0 bad file records processed.
Stage 2: Examining file name linkage ...
950258 index entries processed. Index verification completed.
0 unindexed files scanned. 0 unindexed files recovered to lost and found.
Stage 3: Examining security descriptors ...
Cleaning up 23565 unused index entries from index $SII of file 0x9.
Cleaning up 23565 unused index entries from index $SDH of file 0x9.
Cleaning up 23565 unused security descriptors.
CHKDSK is compacting the security descriptor stream
Security descriptor verification completed.
102266 data files processed. CHKDSK is verifying Usn Journal...
Usn Journal verification completed.
Correcting errors in the master file table's (MFT) BITMAP attribute.
Correcting errors in the Volume Bitmap.
Windows has made corrections to the file system.
No further action is required.
124033023 KB total disk space.
102267364 KB in 501076 files.
261616 KB in 102269 indexes.
0 KB in bad sectors.
820691 KB in use by the system.
65536 KB occupied by the log file.
20683352 KB available on disk.
4096 bytes in each allocation unit.
31008255 total allocation units on disk.
5170838 allocation units available on disk.
Internal Info:
00 61 0b 00 ef 33 09 00 2f 6c 10 00 00 00 00 00 .a...3../l......
99 05 00 00 06 63 00 00 00 00 00 00 00 00 00 00 .....c..........
Windows has finished checking your disk.
Please wait while your computer restarts.
Edit: this is weird but... I created a new user account on my PC, logged into it and logged into MS account in Store and the apps are downloading
Also, in that Windows Logs I found error about Facebook app on this account of course, which seems to be only one not even launching.