Some more observations and suggestions:
The changes add to your game for the most part so good job.
First of all there are a couple of bugs which effect the game quite a bit.
1. If you are holding left or right when you switch to crouching your shots will go diagonal into the ground. This can be frustrating, especially during the boss fight.
2. If you finish the game and decided to play again, you start with the same health as you finished the game with.
-I don't entirely understand the boulder objects I have to admit. I think if you shoot one and it turns not solid, the ones on top of it should drop. There's nothing to immediately suggest anything is different about them after you shoot them otherwise (even though they turn dark blue.)
Also there is a part with a large shaft where you jump up on platforms, and there are a bunch of boulders here. You can actually just jump on the boulders, you don't have to shoot them, which isn't what I think you intended. Perhaps if you made it so you could shoot them you could make boulders fall on top of the player and hurt them. It would make this part more exciting.
You added a weird skull thing, I thought that was kind of cool.
The room where you drop down into a bunch of enemies, it might be a good touch if it's completely dark at the sides until you kill the enemies. This way they stay hidden and when they move into the light it feels a bit more crowded and frantic.
The boss fight feels better, I think you slowed the shots down or something which made it work better. It might be a nice touch as you destroy more turrets to either spawn more enemies or make the guns speed up a bit, just to give the encounter a sense of urgency.
I like to see that you updated your game again, and would encourage you to keep working on it!