This is my strategy. I use the Snake.
First form: You don't have to move left or right. Getting the timing correct, jump/boost up a little just when he charges at you, shoot down, shoot up, and hop to avoid the bones when he lands (shoot while hopping). Use the Nemesis for this bit. After four of these, you will have removed about half of his health. Ballos will jump into the air. Stay where you are and spam the Nemesis directly up as fast as you can. You should be able to kill him before the first lightning strike commences.
Between first and second forms there is a brief interlude. I suggest you walk all the way to the left corner of the room (you can walk through the spikes without taking damage during the interlude).
Second form: Boost up onto Ballo's right eyeball (you can stand on it) and unleash blasts into it. Don't stop shooting, because when Ballos jumps he will throw you into the green demons, and you want your shots to kill them to avoid collisions (which causes you to take damage and jump in recoil, making landing back on Ballo's eye difficult). Depending on choice you can either use your Nemesis or Snake if the Snake is levelled up (because shooting the green demons drops a few XP nachos which you inadvertendtly pick up. The Snake is more resilient to picking up XP, while the Nemesis outputs more damage and doesn't become weaker when you take damage. If your Nemesis gains XP, switch to using Curly's gun). Feel free to use a few super missiles to save some time, because you don't need the whole lot to kill final form Ballos. IIRC, if you levelled it up to max you only need 5 for final form.
Keep track of where your character is and try not to fall off the ridge of his eye, because getting back up wastes precious time. If you're fast enough, you might have killed this form of Ballos when hes on the far right of the room.
Third form: Ballos will orbit around the room and your aim is to destroy his floating eye orbs as quickly as possible. Starting from the right, lead Ballos slightly and use Curly's backblast from behind (Switch to Snake or Rocket Launcher as there may be some XP left from the previous form). When you get to the left side, walk in between the eyeballs and follow Ballos from below, firing upwards as fast as you can using the Nemesis. Repeat until you've destroyed all the eyes. If you're fast you can manage this in 1 or 2 orbits.
Final form: Stand on the floor directly below the side of Ballos. Wait until the pitchforks come pushing out of the ground, let yourself get hit by it, and exploit the temporary invincibilty to boost all the way onto Ballo's eye. When he activates, pump super missiles into him. He should go down quite quickly.
