Some thoughts on the attainment method issue...
Pooling the Throne Room and Palace upgrades into the same system could work if there's a similar number of upgrades for each, but as ManFromMars said, it doesn't feel remotely like we're getting spammed with notifications, so I don't think it would be problematic to have more.
If you'd rather separate them, rather than giving them a random chance to occur on certain events, how about having a metre which is gradually filled, at which point an upgrade happens? ManFromMars mentioned the idea of an accumulation system a few posts up. For example, the Throne Room metre could build up with Culture and positive Happiness (with significant bumps happening for Social Policies, Golden Ages and relevant Great People), the Palace metre building up with Gold per turn and Faith (significant bumps for all the other Great People).
Or, you know, just go with victory points as already mentioned...
Civ 5 has very little randomness in the gameplay design, it's mostly a game of filling or depleting metres. Whether it's visually represented or not, this would fit the game nicely.
This might change the concept of the mod too much, but another suggestion could be that upgrading the Palace makes a small change to the Palace
building in your capital city (for example, +1% Culture, Production, Food or Strength per upgrade, depending on the type).
In this case, it would balance things to make Palace upgrades purchasable via resources (Gold, Faith) rather than happen in a natural progression (or as well as?). It would mirror real-world circumstances in which vast sums of money are spent on aristocratic dwellings while the rest of the country suffers from the expense (Tsarist Russia, modern North Korea).
The thing with the Palace is that its look isn't era-specific, so there doesn't need to be an even, natural pace to it (unlike the Throne Room - you'd feel weird having a stone age cave when you're building a ship to Alpha Centauri).
Ultimately, this system would differentiate the Throne Room, being a reflection of your progress, with the Palace reflecting your gameplay ideology.
One more thing, and I don't
think this has been mentioned, but as of v2 the order of Throne Room upgrades isn't correct (just for the first couple of 'levels').
-Wall: ruined stone should come before rock.
-Floor: smooth, dark stone should come before sandy.
-Front pillars: wood should come before stone. Back pillars are in the right order though.
-Back wall: dark gravelly surface should come before rock; however on my copy of Civ 2 this is bugged and the rock wall displays for the first two levels.
To demonstrate, a few screens from Civ 2 (with bugged back wall):
-Start
-Tier 1
-Tier 2
I'd just like to say though, LOVE the mod, awesome idea and great execution. Massively anticipating the next version.