Your sigpatches are not working, head over to this thread: https://gbatemp.net/threads/sigpatches-for-atmosphere-hekate-fss0-fusee-primary-fusee-secondary.571543/page-50#post-9457839
Regarding problem 1: Try to boot using fusee-primary.bin, don't use hekate if you need these specific patches. You can get the most up-to-date fusee-primary.bin on the atmosphère github release page.
I'm using a self-compiled sys-ftpd (jakibaki/sys-ftpd) on 6.0.1 with ReiNX and it works fine. Didn't get a crash while transferring a lot of files both ways.