Right now I have a running document with every configuration for every game and a sort of change log of how different settings affect performance. It would be way easier if I could just have a config file associated with particular isos. Is this a built in feature? Is it hackable? Thank you!
Nope. Only way you could do it is I guess keep separate pcsx2.ini files and replace them each time for each different game
Good configurations are usually good for all systems. What varies a lot from system to system is the FPS you will get with certain configurations. A stronger PC than yours could afford to have clamping set to extra and preserve sign which is slower but eliminates some bugs in some games, but you could be getting so low fps that you would like to compromise the image quality for getting more speed. That's how it goes usually
Assuming drive space isn't an issue, you can also keep a full copy of PCSX2 with the plugins and configurations you're using for specific games. That's what I do. Each folder should be less than 20MB (~25MB with all plugins included in the default install). Given an ISO is around ~4GB, I find the additional space consumed by PCSX2 to be pretty negligible. It's less than the size of a FLAC file.