I don't know if you were right our if was the community combined help. I entered in the setting and was attempting a reconfiguration of the touch screen and as I saw it didn't work at all. I didn't expect this at all to be the issue but I think that the screen protects are just like a virus. maybe because not once did I think to take off not did I even believe I would affect the rest of my buttons. but once I took it off the touch worked fine and when I returned the menu everything was fine even the d-pad started working again. none of this makes any sense to me what so ever, why would the touch screen affect every other button function in the 3ds, isn't the touchscreen and the button separate, I guess apparently not. the lumas Rosalina menu was crashing but after following Rickens' advice it was gone and the controls did work better. I think it just had to be a combination of a corrupted luma system and a crappy reused screen protector that was the problem. WHat corrupted my luma was probably that SNES CIA I downloaded which might have been corrupted itself. Sorry for bothering the community by giving the notion of a virus, when instead it was a simple corruption of luma, and of course a screen protector that was messing up the controls.
Also, i checked to see if the problem returned when putting on the screen protector and nothing happened, it seems to work fine, I guess this only had to my suspicion that this had to do with a combination of the both, seems pretty confusing to me but I guess that just how it is.