It will take a while to get used to the one sided pedals. The metal plate you removed and replaced is where the cleat contacts the pedal. Maybe it was a bit loose making the noise. Give it some time and just keep practicing clipping in.

I have Ultegra SPD-SL and they are a bit harder to clip in than my mountain SPD's. You could also try getting a second set of cleats to see if they make a difference.