1) How do I keep different preferences for each program?
The two versions weren't really designed to be installed and used independently on the same PC. The original idea was to upgrade from version 2 to version 3, just like all of the previous upgrades. So, like all of the previous upgrades, version 3 uses the same "Data Store" (the same folder for storing tournaments, templates, database, etc), and the same preferences file. Version 3 understands the formats of all files that version 2 saves. The issue occurs when you try to go back from version 3 to version 2, because some of those formats have changed in version 3, and version 2 won't understand them. The preferences file is written every time the program runs (I believe). Once version 3 writes it, version 2 won't understand it anymore. If version 2 cannot understand the preferences file, it will overwrite the existing preferences file with a new one, with all of the preferences set to their default values. Hence the behavior you've described.
During the development process for version 3, I realized people would want to be able to download and try out version 3 (since it requires a new license), and may not want to ultimately upgrade. This is a big reason for the strong recommendation to backup your data before upgrading. If you decide to go back to version 2, you'll have to either lose your preferences or restore from backup. Same goes with any tournaments or templates you load into version 3 and then save, because they'll be saved in the new format and version 2 will no longer understand them. I got so many emails from people who did NOT follow the recommendation and who "lost" their player database (well, I usually ended up manually editing it and restoring it for them), that I released an updated version 2 that understood the database format of version 3.
The workaround is to tell TD version 3 that you want to store your preferences files in a different location. Take a look at section 39 in the user manual (Help tab in the Settings window). The second section under there describes how to override those file locations. This will allow version 2 to use the default location, and version 3 to use a different location.
2) How do I make TD3 stats only count top 10 tournaments? (I'm using points, not score)
Create an Overall Score formula:
sum(top(10, points))3) When uninstalling TD2, should I move my saves from documents/td2 to somewhere else or is it already in TD3 database?
If you plan to continue using version 2 AND version 3, it might make sense to keep them separate. Otherwise, if you happen to load into version 3 a tournament you intend to use with version 2, and save it, version 2 will no longer understand it.
I guess the real question is, why continue to use version 2 if you have version 3?