Hm. Don't know if it'd still help, but the strategy I've been using to beat the 'final' bosses is...
Misery - Stand beneath her when she teleports in, aim up, spam Machine Gun. The moment you hit 80+ damage, start running, jump if necesary to dodge the black orbs. Fire at bats on the way to her as she teleports again if/when necesary, repeat. If she's too close to the ground when she has the dark shield going, fire at her from the side - may as well do some damage.
Doctor - for his first form, it's possible and quite easy to just hover on the ceiling while raining death onto his head, dodging by foot whenever he does his mid-air burst attack.
I'm not sure if infinite flight works without the TurboCharger, but if you manual-fire the Machine Gun, you can fly indefinitely, and you can actualy fire slightly faster than by holding down the attack button.
When he turns into the Muscle Doctor, you can either just fire at him whenever he's not moving ( or, if you're uncomfortably close, try jumping away and turning in mid-air to shoot at him ) , jumping over him when cornered, and spamming at his hands whenever he fires out the bats ( you should be able to take out a good number of them before they leave ) .
If you're willing to take a bit of damage for the sake of speed, just stand next to him with a level 2 Blade and mash the button down. With a good twitching finger, you can drop him in less than three seconds that way.
Of course, the above mentioned strategy of just floating above his head still works.
For the Undead Core, I actualy avoid shooting Misery and Sue - which, I learned, helps slightly, as Misery will only attack you if you hit her first. And she'll only attack one or twice or maybe three times before becoming passive again. Sue's easy to dodge, since she can only hurt you when she's spinning - otherwise she's also harmless. Otherwise, just stay on either one of the pods or the platform at the end of the room, and fire your weapon of choice into Undead Core's face whenever he opens up, unless he's about to fire his giant mouth-cannon. You can try tossing a level 3 Blade onto him just before he fires, so that you can still be doing some damage without getting hit.
As another mentioned, Misery gives you powerups, so if you're not like me and don't care about theme playing, you can pop a few shots at her head anytime you need health or exp.