I only have 1 computer so I have to use it for both emulation and RNG manip. For Mudkip I can't reset the game and start the timer at the same time because only the window I'm currently on registers inputs, so I've been using an audio cue for both reset and choosing Mudkip (I wait for 19 beeps on a 600 millisecond interval since 11400/600=19). But obviously this is far less consistent. Any ideas to make this more consistent? Thanks.

OK, so pressing and holding the reset button gives a white screen and when I click start on the timer both the emulator and timer start at the same time. Is this allowed?

OK, I see FlowTimer has global hotkeys.

Yes, flowtimer has global keys, so you can just run it in the background and possibly have a emulator key binded to the global key as well, like select, also yes, that's allowed, I also recommend using a bios if not already