I notice that when I kill a lot of guys while powered up from Focus Spirit, a bunch of bonuses are listed on screen, like more rupees or rarer weapon drops. Do those go away when I revert to normal? That doesn't give me long to use it. Or do they stay longer?
The bonuses from Focus Spirit last until the player has reached 200 kills. While digging through some forums, I found that user Whitevice had his effects last for the entire level.
I believe Focus Spirit drop boosts apply for the entire level since the few times, I've managed to get two magic bars in the same stage, the drop boosts continued from where I left off. i.e. 1st Magic Bar got me to EXP boost, 2nd Magic Bar got me to Weapons boost.
However, supercheats.com states that Focus Spirit recovery seems to "stop after 200 kills". It is entirely possible that Whitevice completed a level without reaching 200 kills, so the effects lasted for the entire level.
This doesn't mean that the effect can go on forever. The Focus Spirit recovery seems to stop after you reach 200 kills.