It's exactly like you described; first do the 'disclaimer-cal remove View-openmode', then flash back to back.

However I cannot remember exactly what was the command line so that the device gets flashed so that the openmode warning is still off. (I should dig up one of my old N9's and check it...)

About the other problem, crashing of applications when installing stuff; I remember that was a problem which was patched and the patch/explanation should be somewhere on TMO too.