That long? OK. I just did some test with changing font only (once font size and once font shape) and desktop started correctly. It took about half a minute, but most important, I did see some progress. When doing some other changes (like color, transitions, icon set or even reapplying changes after theme change) I can see no progress at all for a long time. As even the system bar is not being loaded (instead there is a black rectangle on top of the screen) I can't even see whether the cpu is working. I also cannot change to some running app (I have always conky running, so I could see what system is doing if I could bring it to foreground).
Will try again and let it do whatever it does for some minutes. If desktop is coming back after some time it's OK, if not, I will try to figure out what system is doing instead.