I appreciate your willingness to make changes! As I mentioned, I have been entirely captured by this game, and have been possibly too obsessed with it recently. I just sent you an email with a few more edits I've found as I've continued to play, as well as requesting the Third Wave supplement.
On the topic of the organization of the rules -- I get that you don't want to move too much of This Space Intentionally (TSI) to the core rules, but to be honest as it is now, the core rules are much harder to play (if not impossible) without TSI. I just think that generally you should consider a major rework of the organization of those first two books -- if you decide to focus on the rules for exploring a site in the core rules and save solar system travel and Operations for TSI, then you should probably move Encounter Designer and Site Designer to the core rules and move Observations, spacecraft movement (from Travel) and Service Risks (from Risks) out. Alternatively, move Map Designer, most of Travel, and Observations out of the core rules and replace them with Missions, Mission Designer, and Operations from TSI. I don't want to make it seem like I'm telling you what's best with your own game, by the way, but I do really think that some sort of reorganization would be worthwhile.
On the topic of names, to be honest on my current playthrough, I've just dropped the Call Signs and Normative Determinism entirely. I've just been using online name generators to come up with names. I totally agreed with your sentiments on why to use call signs instead of names, until I tried actually doing it. I just found that using a random name generator to come up with a real name (i.e. Mission Commander Sandra Romero, vice 'Vacuum Flight') massively increased my investment in the characters and ability to visualize them.