I think that's just a coincidence. I haven't changed that stuff; at least not directly.
Regarding pacifism. I agree that it's a relatively weak civic, don't think it's quite as bad as you say. I don't think it is fundamentally flawed. I think the main problem is that the gold per military cost becomes very big very quickly, and so the civic is basically only viable if you either a very small civ, or are living in isolation. The gold per unit thing is just too big. Even at it's lowest non-zero settings (1 gold per unit), it is prohibitively costly. But it is still a viable civic sometimes. I disagree that the tech is on a bad path. The fact that it is on the way to liberalism means that it's a high-value tech; and the fact that it can be bulbed by a scientist means that it is often discovered relatively early.. often before most of the techs that you mentioned. It's really a matter of play style. Most of the techs you mentioned are good for military reasons... and the civic we are talking about is pacifism. I suspect that you might be a bit of a warmonger in your play style.
If I was to change it, I'd probably change the 1 gold / unit into something like +50% military maintenance cost - which would be a significantly lower cost. Unfortunately, in terms of programming, anything that adds new xml entries is a non-trivial change; because there would need to be new game mechanics written, and new AI to understand how they work. That includes my + maintenance idea, and your + cost per city idea.
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On the topic of the pre-chop feature, I just looked at the code from BULL; it's actually a pretty minor change if I just copy what they've done... but to me it looks like it has a major problem. I haven't tested it myself, but at a glance it looks like this option would cause OOS errors in multiplayer games if not all players were using the same settings. In my view, that's an unacceptable flaw. So implementing this feature isn't just a copy-paste job; it would need to be redesigned.
So, just to clarify, you seem to be suggesting that cities would achieve legendary culture when they reached 50,000 / x culture, where 'x' is the proportion of native culture in the city. Is that what you mean? So, for example, if the city was only 70% mine, then that would be 50,000/0.7 == 71,430.
In response, let me first point out that the number culture points reported in the city screen only include culture that was created by your civ. It does not include any culture from foreign civs. So, for example if the city screen says you have 20,000 culture points, and the city is 80% yours, that essentially means the native culture is 20,000, and the foreign culture is 20,000/0.8 * 0.2 == 5000. (ie. the 80% is 20,000 / 25,000; not 16,000 / 20,000).
Secondly, what I just said is not exactly true either... because the percentage of city ownership is actually calculated based on plot culture, as opposed to city culture. City culture is the culture earnt directly from sources inside the city; ie. artists, cultural buildings, and so on. Whenever city culture is created, it also creates plot culture in all nearby areas - and so if you create culture is a city which is near foreign borders, some of your plot culture will spill in to their land. In most cases, the foreign culture in the city itself is actually zero. So when I said that 80% might means you have 20,000 of 25,000; that wasn't really true, because the 80% is only talking about plot culture. ...
Ok. The main point of my previous two paragraphs was just to make it clear that the culture counter in the city is only counting culture that was earnt by the city itself. Every single point of culture on the culture bar was earnt locally. -- So for that reason, I would think changing to to legendary target to depend on the ownership % would be a bit unnatural, and perhaps a bit confusing.
Maybe it would have some interesting effects on gameplay, but I don't think the effects would be necessarily positive. The main effect would be that it would become adventitious not have your cultural cities on the border of a foreign civ. It would be an advantage to be on your own island away from everyone else. Also, Mercantilism might be slightly more useful, because it blocks foreign trade routes, and thus blocks that source of foreign culture. But in most cases, I think it usually wouldn't make much difference anyway - because unless you happen to have your 3 main cities close to some other civ who is also aiming for a cultural victory, then the city will be close to 100% yours anyway.
The bottom line is that I don't think that would be a good rule change. It adds complexity to the game without adding obvious benefits. It may enable some new and interesting strategies, but the strategies are a bit counter-intuitive. (The best way to win a cultural victory would be to isolate yourself from the rest of the world. That seems counter-intuitive to me.) So that's my opinion on that.
(so you can keep one unit in the city as a garrison) +100% war weariness, +1 
per unit support costs, +50% 
points.
penalties on cities with a large number of military units garrisoned in it. Also maybe have some sort of damage mechanism where units under siege suffer damage?
to 0.
per military unit - I think that kind of stuff sounds tempting at first, but it probably will not have the desired effect. It will probably just result in players leaving them army 1 step outside their city. That may lead to some interesting new gameplay tactics, but I suspect it's more likely to just lead to a bit of player frustration.
