I figure this shouldn't be an issue, since DH Systems was causing the overrides.
I assume this is safe, since nothing appears to be different about my game (same Elite ranking, missions, etc).
4) Now to CCL. I had a hunch from the very beginning that the save file was the culprit with the Distant Sun issue, as I noticed my secondary game has all the computer talking while jumping ("Hyperspace countdown commenced, link established, transfer update complete", and then the countdown), while my game file (which saw a CCL upgrade) only does the count down - and that's it. Any idea as to what in the file may be causing this missing sequence of words?
Edit: I have to now remove the local overrides in order for Distant Suns to work correctly
Edit 2: Thank you Svengali, Cmd. Cheyd and Wildeblood for helping to solve these oddities .