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Great project @Logan Gilbert! Recently, I published a function on Wolfram Function Repository (WFR) called GBIFSearch which I think that it would have been useful for the first part of your project. See a simple example:

ResourceFunction["GBIFSearch"][ Entity["Species", "Species:CanisLupus"], 
                 "OccurrenceGeoRange" -> GeoBounds[Entity["Park", "YellowstoneNationalPark::zc6x9"]], 
                 "OccurrenceDateRange" -> {DateObject[{2017}, "Year", "Gregorian", -5.`], DateObject[{2019, 1}, "Month", "Gregorian", -5.`]} ]

I also submitted a function called BioticInteractions which is closely related to your coexistence graph. It will be nice to compare your results with that function. I will let you know once BioticInteractions is available on WFR.

Do you have plans to extend your project?

Best regards