No worries, and my pleasure.
To your added notes re: #2, your comments again are based on a skewed view of the game from having been knowledge raiding overmuch. That was an exploitative tactic that let people get far more knowledge than had ever been intended. But, that was a tactic used by a small (but overrepresented on the forum) minority of players. This change just brings those players' experience more in line with the experience that everyone else was already having.
The increase in knowledge in the next version is more related to the influx of new technologies and the increases in tenacity of the AI. In that regard, having a bit of extra K seems like it will fit the game well, since there is now so much more that players can do with that K compared to 1.0 of the game. It's the equivalent of having knowledge-raided (under the old model) 5 planets in a game where you capture 20 planets.
Regarding #3, I see your point, but I'm not overly worried about it. The abilities of most of the economic stuff changes with each mark level (just look at the engineers), so I don't think of it as being particularly different. In point of fact it is the most advanced science lab, since it does something that neither of the other two can do. But given that all three are available right at the start, hopefully new players would intuit that it's probably not expected that they will just build the highest tier only. And I believe the description text also notes its intended function, too.
Anyway, hope that helps! And no worries on the questions, it's just been a long couple of days of these same discussions (aside from #3) repeatedly.