2) Merchant Navy still has a production flavor but provides science. (It should provide production still in my view, but if it provides science, it should have a science flavor). (Update: It now still has a production flavor but has science)

4) I think, but I'm not sure, that siege weapons get a double -50% penalty versus land units with a domain penalty in the promotions folder (attached to the city assault promo they get for free) and a penalty in the sql. This might explain why they're so easily slaughtered in combat. I'm testing this one. I'm not sure because the city assault promo is converted over to another promotion (but I went ahead and removed that part of it, just in case).
Something to consider for future use, or as in my mod-mod: What about combining the ASW bonus with the sonar promotion? This would at least give it some much needed umph (and then give it free to the designated ASW units, destroyers and to subs themselves).
More to follow. Still parsing through the files. (feel free to add other bugs during playtesting too).