I have a 1999 kx 125 and the left case intake is considerably higher than the right case trying to figure out what case is the one that was replaced /which one is the original

 

I believe you should be able to find either a match between the frame and engine case number or a source with Kawasaki to mate up an engine number to a frame number.

Either way, looks like you need to get a matched set of case halves.