I am very happy to inform you that your comment of "load them as Power Query queries" made me go back to looking into this option. I had been able to create reference queries that would show me what I needed, but I was unable to link them through relationships back into the data model to allow for the display of the data from different queries within the same pivot. Well, I figured it out (mostly)! I have a locations table lookup that is unique at the Block Name/Code level, but my analyses actually look at the Region and Block Type, not the block name, so I created a reference query that grouped these so that I could then create the relationship needed, but I also had to create a merged columns of the region; block type so that I could base the relationship on that (one to many) but still allow the links to follow through. That being said, I was still having a hard time getting the two separate queries to put data in by reading the species list accordingly, but then I realized I needed a reference query to the full dataset that created a distinct species list that appears in the data, and then link that to those other two queries based on species, and use that distinct species list as the rows. Now I can create one pivot table that has the columns from what would have been two pivot tables.
That is a common, and powerful, technique in Power Query. I didn't mention it but in my little tests that I did with your data that is exactly what I was doing. Take a table with say Species in, strip out all columns but the Species, remove duplicates, add an index column, voila we have a Species table that we can add to the datamodel. We can then replace any other tables that have Soecies in them with a SpeciesId by merging with the Species table, extract the id, anbd remove the old text column. Add more relational, usable.
I think I am at the point that I may need to know more about writing measures, if that is the tool to use. I would like to get the percentage of blocks each species is observed in the pivot as a column.
Whilst I would not siscourage you from learning DAX measures, you might not need a measure for that. Take a look at pivots, right-click an item in the pivot list Values pane, and then click the Value Field Settings. There you can see that you can pivot as a percentage of the row or column. More complex stuff does need DAX, and should you have the time, it will add power to your analysis toolbox.
I created yet another reference query that parsed the data down and provides the # of blocks with data for each region; block type. I have the # of Blocks observed in for each species in each region; block type in one query, but I need a column (I think in that query) that will look for the # of blocks with data in another query that matches the region; block type field to do the percentage calculation. I hope this is making some sense, and if it does, I would appreciate any advice.
Again, I don't understand why you would do this. If you have a table that contains all of the attributes of a block, the type, region, species, your pivot can give you the percentage directly. Am I missing something here?