I would give my eye teeth for block (or lowest available) 2000 to 2010 crosswalk for Puerto Rico along with the same geography pop file. The current 2000 to 2010 crosswalk (which is brilliant, by the way) does not appear to include Puerto Rico.
You’re in luck… at least partly! I can give you half of what you’d like, and I won’t even ask for a single eye tooth. 
We’ve been working on expanding and improving our crosswalks several ways, and we’re not done with the complete project, so we haven’t gone live with all the changes. But one update we already completed internally is to create a 2000-2010 block crosswalk for Puerto Rico, which you can get here.
You’ll find it differs from our existing block-to-block crosswalks in some other ways: including both “GISJOIN” and “GEOID” IDs, using different column headers, and a different readme file. All of these are parts of the general crosswalks revisions we’re implementing to make the labeling and structure more consistent across all of our crosswalk settings.
We still don’t yet provide 2000 census summary data for Puerto Rico through NHGIS (which I’m guessing is what you mean by a “geography pop file”). We proposed to add that in a recent grant submission, for which we hope to get funding soon, and if that happens, we should be able to add this sometime in the next few years.
In the meantime, it’s also possible to get 2000 Puerto Rico block-level data directly from the Census Bureau via the original Summary File 1, via the Census API (which you can access via the tidycensus R package if you’re an R user) or possibly via data.census.gov. (I don’t know if the last of these supports 2000 block-level tables downloads… I’m currently unable to get it to load filter options that would allow me to check.)
OMG!!! This is soo good. Thank you so much.
Jonathan, I just wanted to thank you again for this file. It was exactly what I needed to fill in a hole. We are working on the new Affirmatively Furthering Fair Housing rule and HUD is on the hook to supply the data required to produce and submit AFFH reports. It’s a huge undertaking and I don’t know what I would do without NHGIS. It’s been a good send. Some of our metrics are ‘trends’ and we are looking at 2000, 2010 and 2020, which we are gong to be reporting in 2020 geographies. Some 2000 PR data was the only data I was having difficulty acquiring, but with your help, I think we have it! Thanks again! -Lynn