Hi @namiry check out this thread - https://community.bitnami.com/t/lms-theme-resources-not-loading-path-error/38946/2
I consider myself to be a novice at this, so hopefully my experience leads you in the right direction. I had very similar issues until I walked through that specific thread/reply step by step. Updating my conf/httpd-app.conf file with the proper themes directory was the missing piece for me.
Then after updating the conf/httpd-app.conf file, I walked through step by step the instructions on this thread/reply - https://community.bitnami.com/t/lms-theme-resources-not-loading-path-error/38946/4 . Recompiling the assets was an important step for me.
These 2 threads/replies allowed my stock stanford theme to finally load properly.
I then ran into issues when trying to customize my stock stanford theme's scss files. As soon as I tried to make broad changes to the scss file, the files wouldn't compile properly. Rather than spending hours trying to figure out why they weren't compiling properly, I decided my time would be better spent for me to just start from a blank scss file and slowly build up a new one. This solution proved effective and I finally have a working customized theme.
Just a note on your Cyberduck issues (I also had these when using Transmit), I'm guessing it might be a directory write permissions issue, which was the case for me. I'm not sure if there is an easy solution to using Cyberduck and switching to "root" using the command "sudo su". On my Mac, I resolved to using a hybrid method of WinSCP (via CrossOver), Transmit, and Command Line depending on the task I am trying to accomplish. It's messy, but it works.
Hopefully my experience helps you or someone else. Like I said, I consider myself a novice this and apologize in advance if I didn't explain it properly or didn't use correct terminology. Community, please feel free to correct any of my mistakes :-).