Congratz on your new life! I remember the time I applied for a Schengen Tourist visa through Italy and I had to visit the embassy at least twice because they would say some documents were missing.

I know how it feels like when a simple bureaucratic issue with a visa can affect your whole life. I had a PhD offer from the US but had to wait for administrative processing for six months, so I couldn't go in the end. So you are not alone :)

Greetings from Cape Town :)