Wow. I just pulled off a 99.8%. Here were the secrets I gathered to get there:
There are two kinds of snakelike enemies. The ones that pop halfway out of the ground and fire at you while staying rooted in their holes. You have to take care of those ones fast, because they retreat after firing one shot at you. If you take them out as fast as possible, they don't fire that shot. They have 20 hit points each.
The snakes that fly through the air are totally different. Whoever said to shoot them in the head was RIGHT. Whoever said to use overdrive power on them was WRONG WRONG WRONG. If you focus manually on their heads, they fall apart SUPER FAST. If you use overdrive on them, the auto-targeting wastes all your time firing at the rear, and often doesn't end up killing them, and can make you miss all kinds of other surrounding enemies that fly by while your shots are getting absorbed by the worms' butts.
Also a concern are the X-shaped enemies that tend to fly straight past without stopping. I just memorized where they all were. Most of them can be fired upon well before you actually see them.
I didn't take any extraordinary care at the giant cylinder. I just blew the thing up, and missed plenty of the little spawnlings. Same goes for the bosses. They're all just graded as pass/fail. No need to hit every single one of their tiny little parts.