I think you know more about Chan Chan than I do, so I think it sounds like a great idea. If you want to help that would be great too. I will try to post a new master file so you can download it tomorrow. I am also thinking about breaking the music out of the mod and have it as a second download. The file is getting really large and I saw another mod did something similar, I just need to figure it out.
Awesome! South America has the potential to be really interesting. In Chan Chan, each successive king built a
Ciudadela - a sort of palace/administrative centre with high walls that was basically laid out like a maze, with every winding passage watched over by numerous administrators in podium-like
audiencias - which served as their residence and administrative headquarters in life and their tomb in death. It's probable that each
Ciudadela continued to be used for administrative functions and the training of bureaucrats, sort of like a government agency, university, mausoleum and perhaps temple to the dead king rolled into one. At the height of Chan Chan's power, Qusqu was a tiny mountain kingdom. Around 1066, Chan Chan had been around for about 166 years, so it was nearing its height.
The rulers of Chan Chan built the Chicama-Moche canal, a 70 km canal connecting the Chicama and Moche rivers to ease communication and irrigation across their realm, which was concentrated in the river valleys of the Atacama (though it probably never actually worked). Their taxation system, wherein most vassals paid taxes in the form of labour for construction projects, was probably copied by Tawantinsuyu after it absorbed Chan Chan. Canals could be simulated with buildings easily enough, and the corvée taxation system might be very well simulated by the new tribal construction mechanics from Charlemagne, using prestige rather than gold to build.
The Chimú religion held that the Chimú were descended from the stars. There appears to have been a caste system, consisting of an endogamous royal caste descended from certain particularly sacred stars. Below the royalty was the lesser nobility, who inhabited the 'intermediate' class of structures at Chan Chan, which resembled
Ciudadelas writ small. The nobility perhaps provided the administrators who worked in the
Ciudadelas, as well as provincial governors. Then there were the commoners, who lived in the Small, Irregular, Agglutinated Rooms (SIARs). They were essentially a population of craftspersons dependent upon the royalty for patronage. Chan Chan's metalworkers were particularly esteemed, and were all relocated to Qusqu following Inka conquest. As with the Indian caste system, Noble and Common caste could be linked to castle and city holdings respectively. Royal caste could be a prerequisite to inheritance.
Chan Chan seems to have been unique in the scale of construction, but there were regional administrative centres whose architecture in some respects resembled that of the intermediate structures. It might be an idea to have the primary holdings in most of the Chimor region be cities, requiring the player to construct a castle as an administrative centre and switch it to the capital by decision, event or in the usual way (revoking the 'county') or else leave the subjugated village (i.e. city) rulers in charge of their provinces.
There are some difficulties, particularly, as is often the case with Precolumbian America, with the language. We have the names of some of the rulers...
- 900?–960? Tacaynamo
- 960?–1020? Guacricaur
- 1020?–1080? Ñancempinco
- 1440?–1470 Minchancaman
...but sadly not much else, to the effect that a lot would have to be made up. One idea might be to use the English translation of Spanish terms - I find the use of the Spanish terms themselves sort of malapropos for a mod about the Precolumbian era, while the English term is less jarring, being plausibly just descriptive of function ('Citadel' or 'auditorium' instead of '
Ciudadela' or '
audiencia'.) Fortunately, in the case of the Inka, the terms relevant to administration are much more readily available to us, by merit of their being the greatest conquerors and state-builders of the Precolumbian world. The Quechuan language family and its oral tradition are alive and well in the present.
The administration of Tawantinsuyu could be modelled using game mechanics in a way that would make them very unique to play. One of the main motors for Runakuna/Nunakuna (the self-designation of the so-called 'Inka') expansion was the split inheritance system. Because the Sapa Inka was considered divine, and therefore immortal, the personal holdings of each Sapa Inka remained owned by that Sapa Inka (i.e. by their mummy) following their death. New rulers did not inherit their father's personal property; it remained legally (to the extent that the term is applicable) the property of the dead ruler, managed by the royal mummy's cult. Mummies played an important role in ceremonial life, being dressed up, ritually fed at feasts, paraded around, and so on. Province modifiers severely limiting the levies and taxation from provinces, applied after the death of the ruler who conquered them, could simulate that system, requiring the player to hand out their previous ruler's holdings (except in the core area around Qusqu) and conquer new land if they want to have productive provinces with large levies.
The administrative strategy of Tawantinsuyu was very variable over time and between provinces, in some places being very territorial (involving direct occupation and centralised administration) and in others being very hegemonic (closer to feudal vassalage, with subjugated rulers remaining in charge and autonomous so long as they paid their dues). This could be modelled using crown laws, CBs and holding types: a CB that directly occupies all holdings in a territory could be used to allow the player to give that territory to a city vassal, representing a direct governor controlled from Qusqu. Given that the main concern in areas occupied territorially was the extraction of wealth and construction of infrastructure, CK2's city ruler mechanics are quite apropos. A crown law could then be used to control whether directly occupied territories are focused on levies or on taxation.
A different CB which vassalises the former ruler could be used to model the hegemonic strategy. Where an entrenched and cooperative elite existed already, Tawantinsuyu left them largely to run their own affairs. Rulers of such provinces were required either to send labour to Qusqu or to send soldiers to fight for the Sapa Inka, not both. It might be a bit harder to model that, but perhaps honorific titles could be used - one set of crown laws, tied to one honorific title, would increase levies and reduce taxation; another, the opposite.
Religiously, the Sapa Inka should probably be a secular religious head of the official state religion, which was focused on the divinity of the Sapa Inka and the royal mummies (a good, flavourful honorific title would be Curator of the Royal Mummies, or something like that, providing piety and a boost to temple vassal opinion). Tolerance of other religions should probably be very high by default. By and large, Sapa Inkas did not attempt to convert conquered populations. They did build ritual centres and hold regional festivities in honour of the royal mummies and the god king, where participation was probably compulsory, but aside from that, subjects of Tawantinsuyu were free to practice their native traditions and customs. The religious authority of the Sapa Inka could perhaps, then, be modelled using festival decision mechanics (like Hold a Feast, Observe Ramadan, etc.), where refusal of a vassal to participate would be tantamount to a declaration of open rebellion.
I have more ideas, but this is already very long!

I go back to university soon, where I have access to a universal library, so I can also look into the other South American cultures. In the period the mod is set in, the Aymara Kingdoms were the most significant South American power, but I know very little about them. If the map could be expanded further into Bolivia, the Yampara could also be included; later on, they were very important Inka vassals, given special status within the empire for the contribution of their soldiers to the subjugation of Chimor, which was then Tawantinsuyu's chief rival.
Edit: As for separating the music, I think you just have to create another mod folder and .mod file, put all the music-related stuff in that folder and write the .mod file to replace the relevant directories.