These 2 wires go thru the roof towards the back of the bus and then loop back in with nothing attached, I believe I followed the white one to a ground up front. I think there might be a leak here so if they aren't of use I'd like to pull them and seal the hole.
They probably went to your strobe light. If your dash has a switch for the strobe light you could keep those wires and utilize the switch for something else.
I'd maybe consider a disco ball. Really I'd just yank em. If after everything still works then you did good. I have some roof leaks myself. Anything that was on the roof i removed. And am in the patching process. Is there a fool proof roof patch method?