At quick look, you are customizing the wrong device interface plugin. Try the the KoboTouch or KoboTouchExtended (if you are sending kepubs) driver and place your collection information on the second page. The place you placed your collection information is to control the filename and location of files sent to the device. In other words, every book you sent that is in same shelf and series is being given the same name so you are overwriting most of the files with the next file being sent.
For me, the filename field is filled with: Elibrary/{author_sort}/{title} - {authors:sublist(0,1,&)} which gives me usable file names. I don't use collections preferring search.
I've attached a couple of images of what I see with the KoboTouch driver. I would suggest you go back to the
Kobo Shelves and Collections wiki and re-read it carefully paying strict attention to the second step.