I'll try to make this short: There's an old game that runs a bit faster than it should, which makes the real time inaccurate (luckily, the game has its own timer, which appears at the end of each stage). There are tools to change the FPS, but 30 is sill too fast and 29 is too slow.

This is a game without any demand reall which I mod (Little Fighter 2), I just want to get advice on what to do. Right now, the important time is IGT, which is sum of all stages together.

As long as all runs are using the same timing system, it shouldn't matter; time is relative. In fact, an in-game timer is usually preferable because it tends to count at the same speed relative to the FPS of the game, so although the game time may not correlate precisely with real time, in-game timers will generally be accurate relative to those of other runs of the same game, and that's what matters.