I had the same issue with the N64 emulator, which was fixed by reinstalling mupen64plus from source (after updating the setup script first) from retropie_setup.sh. That fixed the black screen thing for me, but i’m still left without fullscreen for now.
As for the black border thing, does it exhibit the problem all the time? Or just particular emulators? Have you tried mucking around with any of the output settings in es_systems.cfg?
Can’t help you with the controller thing for now.
I’ve got mine with a 256 GPU split, which seems to be working alright for now. There was no rationale behind this number, it just sounded cool.