How to keep track of line numbers in response to reviewers?
This is always a pain, but I find it's not actually hard to deal with, just somewhat tedious.  My method for doing so is rather low-tech: I keep a copy of the old document to be able to track the old line numbers, then leave all of the line numbers in the response as XXX until I am done with the revision.  Then, for each entry, you just cross-index in both places and write both line numbers, e.g., 


  'co-occur' was replaced with 'correlate' in line 245 [prev. 243]


For minor wording/grammar edits, however, I usually don't actually respond in such detail, but simplify both my life and the reviewers by just saying something like: "thank you, fixed"