Specifically, I'm interested in the cultural differences between civilizations meeting each other for the first time and the reactions of both sides to these events. It seems like there were many normalized concepts in Western Culture that the Spanish/Europeans saw as blasphemous and wrong, but I can't find anything on how the natives responded to this. The vast majority of non-abrahamic religious texts are alleged to have been burned and destroyed by the invaders upon discovery, and it doesn't seem far fetched to assume other parts of that world are lost to time for the same reason. The conquerers also seemed to view gender-variance in tribes (i.e. anything except the patriarchal and heterosexual two-role binary system) as similarly blasphemous and strange, though it has been documented that this part of the culture (like most parts) developed with varying results under various isolated tribes, until the monoculture was irreversibly enforced by the Eastern peoples.
While searching through Wikipedia (I'm still early in learning good research techniques) I realized that a not insignificant amount of the citations point to information written by the colonizers themselves about their experiences in the 1490s-1500s meeting these people and living among them long enough to learn their ways. The vast majority of historical books available now are written by archaeologists and researchers about things that happened thousands of years ago, and I would be interested to see a less removed perspective on this subject.
I'm specifically trying to research reactions to "transgender" cultures like the North American Nádleehi and Polynesian Mahu peoples, which seemed to be almost invariably suppressed and intolerated by people from the eastern continents. However, just any help at all with researching ancient cultures from a more direct and less futurist gaze would be of interest to me. I am also trying to learn about ancient religions and gods, and what the western natives had/have to say about primordialism and the origin of humanity, as contrasted with what seems to be a completely different story believed and enforced by the Easterners. Were there willing religious converts on both sides, and if so then how were they accepted? Are there any accounts of European missionaries abandoning their customs to practice New World methods?
First off, I'm always going to recommend u/Kelpie-Cat's answers on gender in the Pre-Columbian Americas if that's something you're particularly interested in. Their answers (more linked on their profile) will have resources more directly related to that part of your question.
Edit: Realized this would be a great place to link the "Monday Methods" series on finding and using sources. The whole series is worth a look, Parts 3 and 4 focus on primary sources. Also check out u/Snapshot52's Monday Methods post looking specifically at indigenous sources.
To your point about wanting to find primary sources for your research, there's a few things worth noting. Firstly, many Indigenous groups in the Americas physically recorded their history in ways that a colonial audience wouldn't immediately recognize as writing. That means the study of those societies has often been left to archaeologists (once again, thanks to u/Kelpie-Cat), though that disciplinary divide is becoming increasingly blurred in the Americas.
Even for groups that didn't physically record their history, Oral traditions helped record the past. Unfortunately, I wouldn't know the specific places to point you towards for North America or Polynesia, that's a bit outside my wheelhouse. That said, Polynesia has long been a hotbed of back-and-forth between scholars over the role of oral history in reconstructing the past. See, for example:
Kirch, Patrick Vinton. “Voices On The Wind, Traces In the Earth: Integrating Oral Narrative and Archaeology in Polynesian History.” The Journal of the Polynesian Society 127, no. 3 (2018): 275–306. http://www.jstor.org/stable/45017397.
As your question points out, we also have the issue of sources being intentionally destroyed by colonizing populations when they did recognize them - the Spanish often framed this in terms of wiping out "idolatry", and it wasn't just limited to texts. As your question also points out - sexuality and gender may have been areas of particular concern.
The biggest issue, though, is that primary sources are difficult to work with.
The vast majority of historical books available now are written by archaeologists and researchers about things that happened thousands of years ago, and I would be interested to see a less removed perspective on this subject.
I don't mean to be rude, in fact I applaud your desire to engage with this history, but you need to be careful of falling into the trap of trying to engage with primary sources that you don't have context for. Documents written in the past are not somehow less biased or "more direct" than secondary sources written today. The fact that you acknowledge you're early in the research process makes me think you might want to spend a bit more time establishing this context.
Like you noticed, many of our early documents come from colonizing authors - conquistadors, missionaries, administrators, etc. Obviously, you need to account for their eurocentric bias when you read what they've written. Creating a context for these early documents - for the reasons noted above - therefore requires deep knowledge of archaeology and/or oral history to "unpack" (I hate this term...) the text.
The same is true of indigenous-authored works. Take for example, Guaman Poma's El primer nueva corónica y buen gobierno (because it is in my wheelhouse*).* Given the fact that its's written in Spanish, it obviously post-dates the Spanish invasion of the Americas. However, due to the indigenous identity of the author and his seemingly apparent concern for abuses perpetrated against indigenous Andeans it would be tempting to see his text as a "more direct" or "less biased" representation of indigenous thought in the early colonial period. At the same time, it's necessary to realize that Guaman Poma was descended not from a 'common' indigenous family - but from a noble family that had maneuvered to maintain some sense of their position even after the Spanish takeover. A great deal of his writing isn't concerned with arguing for the dignity of indigenous people as a whole - but for the dignity of the indigenous nobility and the legitimacy of their political power. His letter to then King of Spain Phillip III - which is what the nueva corónica really is - is couched in the rhetoric of a petition. But, it's Guaman Poma's noble heritage that gives him the authority (and the necessary access to Spanish language education) to write such a document in the first place.
Texts like Guaman Poma's do help counter an overwhelmingly Spanish perspective in the historical record. At the same time, we can't assume that early documents, even when produced by indigenous authors, necessarily speak to a common experience. Like all other historic documents, they need to be placed in productive dialogue alongside other lines of evidence (archaeology, oral narrative, etc).
Like I said earlier, I think it's great that you want to dive into these topics. I especially appreciate when people want to dig into the primary sources. That said, I'd recommend keeping some of those secondary sources handy at the same time. In fact, the citations at the end of a secondary source are where I'd recommend you start your search for primary sources. When you pick a primary source that looks interesting, start your reading session with the secondary source you where you found it open on the same table: flip back and forth, cross reference. You'll come out ahead by understanding primary sources in a wider context, and that wider context only comes from those 'far removed' scholars writing in the present.