First of all, even if the effect is small, I think all leaders should care at least something for all the usual relationhip modifiers: same/different religion, using favourite civic, open borders, resource trades...
No problem to do this, though religions are a special case here - even if the effect (both positive and negative) is set to 0, there will be still a +1 or -1, if the AI has the shrine of its faction religion (this seems to be hard-coded, at least it is not accesible from the leaderhead.xml) - which is quite common for PF, especially after the change regarding religion spread.
One example: I think Santi and Zak should care about people following their favourite civic. I would suggest that Lal cares more and Yang cares less (a fellow dictator is still a rival), but that the other factions should care an equal amount about their favourite civic.
I don't understand why you made Yang and Zak ask more frequently for a religion change. Especially Zakharov, of all the factions it seems he would care least about the five religions/ideologies. His ideology is knowledge and free flow of information. My suggestions would be: Dee and Miriam care most about religion. Zakharov cares least. The others are in the middle group. This counts for both same and different religion. Exception: Lal. He is in the middle group for sharing a religion, but cares just as little as Zak for having a different religion. Again, I do feel they should all care at least
something.
I did those changes because of the recent discussion about "religion=ideology for some leaders?" - that's why I said that point always causes confusion for me
But I understand your logic (though I would seen Morgan as a similar character in this regard - he might care for others running Free Market, but for religion? Except we think of him as seeing religion as a kind of business...)
I would suggest an impact of +/- 2 (weak), 5 (middle) and 8 (strong), reduced by one for religion because of the shrine impact. Sadly there is yet no possibilty to give a penalty for running the wrong civic
I noticed Yang now remembers it longer if you gave him tribute.
Do you know how relationship boni/penalties with a memory limit work? I've never really paid much attention to those. I don't see a way to affect the height of the relationship effect. Am I right you can't currently affect that?
No, it is already possible to set how strong the impact on relations should be - everything under "MemoryAttitudePercents" deals with that (so my change for Yang just means that you get +2 for each accepted demand or request) The question of "How long does an effect last?" is set under "MemoryDecays" (which I haven't touched yet), though not all factors listed under "MemoryAttitudePercents" appear here - and the missing ones (like -3 for declaring war) are the eternal boni/penalties.
There is one item for which it is reversed, it is "MEMORY_RECEIVED_TECH_FROM_ANY" - I assume it deals with the penalty for trading with the worst enemy, but I don't understand why I can't it strength (maybe it is tied to the postive impact of tech trading with that leader?)
I assume that the "eternal effects" can be turned into decaying ones, if the needed tags are added, but I haven't tried (BTW, I would suggest that for for some things like the war declararation - this should take extremly long to wear of, but it should be possible).
About decaying...I'm pretty sure that the numbers are 1/x chances per turn (and not fixed time periods in turns), though I'm not sure if the chance hitting means the entire boost/penalty is gone or just one modifier point (though I supect the latter). There is info about this on civfanatics, but it is not always 100% clear and reliable...and I have to admit that I haven't tracked this down enough in game yet to say with certainty.
Also what happens when you for instance trade tech while you already did the same thing recently? Do you get the relationship bonus twice, or is the period before the bonus expires just extended? If it's the latter, I'd consider making it (in the SDK) so that appeasing Yang gives a higher relationship bonus, not just make the bonus last longer.
The positive effects of tech trading are a bit complicated because they can effect two modifiers - "You shared your technological discoveries with us", but also eventually "fair trade relations"...but luckily I digged up a source where both are explained:
http://forums.civfanatics.com/showpost.php?p=6801315&postcount=380
You have shared you technological discoveries with us
Depending on leader we get between 0.05 (Asoka (!), Bismarck, Isabella and Toku of those that could be in the game) and 0.2 (Mansa, Peter) per tech traded to that AI. Decays with 1/100.
Fair Trade
A complex calculation depending on three things:
1) the total value of all things given for free to that AI: iGrantValue
2) the total value of all things traded to that AI: iTradeValue
3) the number of turns we have known each other: iTurnsKnown
The total bonus is then (iGrantValue + iTradeValue/3)/((iTurnsKnown +1)*5), but capped at +4. In other words this value will deteriorate over time, unless we add more trades to it. The calculations of the values is very involved, but I can list that too if it becomes necessary.
You have traded with our worst enemies
The calculation is very similar to that above, except the constant factor in the divisor is 10 instead of 5. In other words, we can trade twice as much to a worst enemy before we reach a certain modifier, compared to the Fair Trade. Note that the worst enemy can switch, but things added to iGrantValue and iTradeValue never disappear, they only get diluted by passing time.
So "Fair Trade" is clearly more "hardcoded" and capped at +/-4, while "Shared Technology" stacks theorectically unlimited (and you can easily affect how much each traded tech effects it) - however, both modifiers detoriate over time.
So for your question - I believe in terms of fair trade "overflow" just extends the time before detoriation (if I understand the formula correct), while for shared discoveries yout get the full effect.
The same thing could be done for Zakharov: the relationship bonus for trading techs with him could be much higher. Someone suggested a while back that Zakharov should be able to ignore tech brokering restrictions. I considered that a bad idea because then the human players would be disinclined to trade techs with him, the opposite of what I'd like to achieve.
If trading techs with Zak would lead to a much higher relationship bonus however, then it would be worth still to trade techs with him, even if it carries the chance he will broker one of your techs.
As said above, that can be easily done and makes perfect sense for me.
BTW, I always play with "No Tech Brokering", so this might influence what feels right (also true for "Aggressive AI", another "default" option for me...)
Back to Yang: IIRC the AI only asks human players for tribute. So if the main way to please Yang would be to pay him tribute, then Yang would be unable to get along with other AIs. So I was thinking Yang should also have a better opinion of players weaker than him - they're harmless, they don't form a threat to his power. Yet at the same time he should still be just as willing to attack those weaker than him. (Is this possible?) So if a weak AI faction was close to Yang, the way to continue those 'good relations' with Yang would end up being forced vassalization...
Great idea

Thats the kind of feedback needed to develop the personalities

It's definitely possible to do that - though it is important to consider the various parameters which could have an effect on this desired behaviour:
1. As you said for "liking" weak factions: "iWorseRankDifferenceAttitudeChange"
2. The war parameters - chance to declare a certain type of war per turn (I made him already a dogpiler) and the power ratios (maybe restrict a "total war" - the one I think which most likely will lead to capitualation - to weak oppponents?)
3. Good relations and still willing to attack...this is mainly achieved by the "NoWarAttitudeProbs" (for strategically planned wars) - here it can be set that "pleased" or even "friendly" relations don't protect you (completely) from an attack, but also by the "DeclareWarThemRefuseAttitudeThreshold" - here you can set the attitude treshold for wars a leader gets dragged in. So we could even differenciate regarding why Yang attacks a weaker faction, he has good relations with - rather/only because of his own decision or because somone offer him something? Maybe we could use this to make him different to Santiago.
Summarized, this would mean there's a clear and distinct way to please each leader:
Deirdre/Miriam: sharing religion
Lal: sharing his favourite civic
Santiago: sharing wars
Morgan: trading resources
Zak: trading techs
Yang: paying tribute
I will rework the file following that guide.
As a final note, why does the AI seem to sneak-plan wars more often when refusing a demand compared to vanilla Civ, even though the odds for it are lower here? Or am I just paying more attention to it now?
I'm not sure. Is this still your impression after the AI fix regaring war preperations? I suspect that the few declarations which happened before the fix were mainly diplomatic ones. In BtS the chances might be higher, but I guess they just don't have an effect as often - because more strategic declarations happen. Difficulty might have an effect as well...what level do you play? PF on Emperor leads for me nearly always in a state of being weaker and getting frequently extorted, but overall it is the level for me to have a competitive AI til the end game. It could be also just because the extortion chances are generally higher - 5 out of 7 leader are 1/100 or below...and those 5 are always in the game. Standard Civ4 offers more leaders (54), of which only a part gets randomly drawn for most games and 21 of them are 1/1000. Maybe I should tweak those values again?