Okay, I gave it another play, and I think that the game is definitely improved by the changes that you made! ^_^
Oh, one thing that I forgot, related to collision: When the player collides with a small step, it might feel better to just have the player automatically move up it, rather than having to jump up every single time.
In other news, I got to the boss! It's a rather cool idea for a boss, I will say!
I didn't beat it: It took a while for me to find a way to reliably hit it without getting so close that I was immediately destroyed, and even then, the seeking shots that it fires don't time out, sometimes leaving me dodging them for a while before they hit the environment! I also ended up with a problem in which it didn't reset its second phase (which I gather gives it a bayonet for melee damage), meaning that I immediately died on attempting to restart the fight!
Still, it's a creative concept--I do like that it initially presents as a weapon-pickup, only to turn into a fight! ^_^