Eliminator,
CFs are not exactly the same as PJ64 1.4. In 1964 some CFs can make certain parts of the game too fast even when some slower things look just fine. The incorrect CFs in 1964 often results in
incorrect timer speed in games (the seconds timers go too fast
for example, instead of 10 9 8 7 6 5 4 3 2 1, it would be 10987654321), so make sure the seconds are not going "too fast" .

In PJ64, even when changing the CFs to any setting, at least it usually doesn't muck up the timers in games.