Thank you for the responses all, greatly appreciated.
I don't know how you are collecting information on all PRs, but I doubt the information on very old PRs is correct, as that data just doesn't exist anymore. If you want to check how accurate very old data is, you can compare your point rankings of late 2000 here. You'll find some more historic rankings here. Comparing your All Time Leaders to the Goldeneye Champions page on speedrunwiki, you'll find rather big discrepancies between the two, mainly for old players.
Thus, it might make sense to have your tool start displaying the points as shown in the screenshot you provided only from a point of time where the PR info is fairly complete and use the speedrunwiki data for the "All Time Leader" day count on the years before that. I guess that would probably be something around 2011, but more knowledgeable eliters will be able to give better guesses than me.
Thanks for those links, those ancient scores are much better than the ones I've been calculating.
The "Goldeneye_Champions" wiki page is great, though there seem to be a few anomalies:
1. Wiki says "Wouter, 2001.9.1 - 2003.12.24 (844 days)"
However the snapshots on following dates have Randy as the leader:
2002-04-18 -
https://web.archive.org/web/20020418021456/http://www.the-elite.net:80/GE/elite.htm2002-06-07 -
https://web.archive.org/web/20020607135739/http://www.the-elite.net:80/GE/elite.htm2. Wiki says "Illu, 2007.1.10 - 2007.4.12 (92 days)"
However the snapshots on following dates have Bryan as the leader:
2007-02-08 -
https://web.archive.org/web/20070208064051/http://www.the-elite.net:80/GE/elite.htm2007-02-19 -
https://web.archive.org/web/20070219055235/http://www.the-elite.net:80/GE/elite.htm2007-03-21 -
https://web.archive.org/web/20070321152240/http://www.the-elite.net:80/GE/elite.htmWere some runs of Randy and Bryan later disgraced / proved false and thus the real point leader was retroactively changed? If so anyone know how much I should drop their point scores and during what rough period?
Separate to these, I can see some other players have had drops in scores over time, so this wouldn't be unusual, eg. Ryan and David have massive plummets for short times with returns greater than before, smaller dip for Bryan (see pic below), presumably these are due to runs being removed then better times being posted shortly after (if anyone has a different theory please let me know). I could easily plug these gaps by interpolating the scores in-between, or keep them as-is, depends on the reason for the drops.
Edit: Another strange sudden change in score is Karl Jobst from 10th in the 2004-06-09 WayBack snapshot to completely non-existent in the next one, only to return to the charts again in 2006-02-17 - did Karl ask to be removed from the pages or something? This one is less important as he's not in the top few ranked players during that time, but still curious.
Edit2: Karl confirms he disappeared due to range-quitting during that time.

Fortunately, the point in time where I transition in the visualisation from the old wayback scores (smooth curves in this pic) to the new calculated scores (jagged curves in first pic) is quite seamless, giving me high confidence that the retroactively calculated scores for the modern era are quite accurate.
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For the super-ancient period between 1997-08-25 and 2000-04-22 I'm just going to display the three players Sterling, Martin and Zwartjes (with no Y-Axis numbers) since the only data I have for that period is the relative ranking of these three players. If anyone knows anything else about this period, that will be useful for the visualisation.
By the way, if you collected all PR information on the Elite anyways, it would be cool if you could dump all that info in a txt file somewhere. 
I'll happily share some data if the mods are fine with it.
The data is in the live database, deleted times are still in there too
Is this live database available anywhere? I'm currently inferring some deleted times from the WayBack machine but it's not completely
accurate as the page snapshots are only available sporadically there. Having the actual database info will improve the accuracy of the chart slightly, accurate created_at and deleted_at timestamps of all PR history would make the chart 100% accurate.
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Thanks for the timezone explanation vitorr, appreciated. I think I'll just live with the time postings being accurate to +- 1 day, it's impossible to discern a single day from the scale of the chart anyway.