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Right now I seem to be able to get PCSX2 to keep everything inside the program folder, except for the .inis. They insist on going in [username]/Documents/PCSX2/inis

Is it possible to add a line to a config file or run the program with a certain parameter to make it use ./PCSX2/inis for all config files (including plugins')?

Just use the binary package for that, it will only use files on it's folder (unless you change it manually that is ):
http://forums.pcsx2.net/Thread-PCSX2-0-9...ows-Binary

Ah, portable.ini in the main folder was all I needed. Cheers!