That application which gave you the three choices on boot, is it Backup Menu? Because if it is, you are in luck, as you might be able to make your system bootable just by copying a backup image to microSD. I think RobbieThe1st (the author of Backup Menu) posted some backup images from a fresh system.

If you reboot with the keyboard slid open, do you get the Backup Menu prompt?

If you do, report back, but don't do anything yet (you might want to FSCK your partitions before doing anything more drastic).

BTW, the problem you are having points IMO to a problem with your /home/user partition. I might be wrong though.