The pop could just be the adhesive holding the logic board releasing some tension. Those boards are held down tightly and when you pry it up, it does force the adhesive to let go somewhat. If the sound was more of a snap, then I would be concerned about pcb damage. At any rate, you’ll know when you re-assemble everything to test.
As for the LCD, be very careful when cleaning it as it is easy to damage. Start by blowing off any glass dust with compressed air. Then use a fine brush, like a camera lens brush, to remove as much as possible. Then use an optical cloth to get rid of the rest but avoid pressing down hard on the surface until everything is pretty much gone.
A LensPen works really nice and there is a larger, square version of the LensPen (ScreenKlean) that does a great job on iPad LCD’s.