I enjoyed this! You managed to make the level a little more taxing (though the third room is arguably easier as Chaddy said - more on this in a bit) whilst keeping with the thematic structure of the game's original levels!
A couple of points to make though:
1 - The first room is great. I love the 'time attack' routes you include that allow you to shave off a few seconds with a greater risk element involved - don't change a thing here.
EDIT: It's possibly to get trapped in this room and have no escape (short of Esc-F2ing); it's where the Deleets spawn - I appreciate that there's a great pit of 127 damage spikes inbetween, but you can take a hit and run through them and fall down. I appreciate it's not something you can really circumvent beyond perhaps including a death pit of spikes at the bottom so the player has a means to die, but then again, it's what Esc-F2 is for... ;D
2 - The block room is an interesting one. I would lower some of the platforms from the ceiling; whilst I'm fully aware that it's possible to do this room without being hit, it involves even more luck than the original version (the falling block configuration of which could be utterly obnoxious at times), as the blocks can fall and there's very little you can do about it - that said, that's precisely why you gave the player 46-51 hit points. ;D
EDIT: I found a bug in this room too - you can fall out of the level and not trigger the 'death' sequence underneath the... this is kind of hard to describe 'the four blocks', where there are four small blocks placed diagonally from each other about half-way through the level. That's about the worst description ever, but hopefully you know where I mean. Just drop down under there and you'll fall infinitely (until you hit reset).
3 - The third room is undeniably a step down in the difficulty department. The danger of having lots of Butes spawn is that experienced players can take them down with relative ease and then grab the powerups they drop - this isn't always the case if you use spikes as a detterent (which you do on occasion); the most notable example of which is the 'Bute Storm' after the skull platforms (I really liked those, BTW), where I just shot them all down , taking 10 damage in the process and getting back about 12 HP from the hearts, owing to the nice solid platform which acted as a nice pedastal for the powerup drops to rest on.
Addtionally, the third room is very open. I haven't tried this myself as I only had a single play through the mod, but I suspect that it's possible to just outrun all the Butes using massive Booster abuse; I think this is why Pixel had so many timed barriers - so you couldn't just charge through the level without some repurcussions (although if you play your cards right...).
EDIT: Yeah, I just speedrun this level now, and you can clear this room in about 15-20 seconds - by the end of it, you've got literally hundreds of Butes to deal with, but if you've been careful in the first room, you can just jump through them
4 - Just reading 'Welcome. I am Ballos. You die now.' made me chuckle; this in part due to the fact that I had to mash the Z and X keys and listen to his emo rant several hundred times in my many play throughs of the original level. Similarly with the uh, 'new ending' ;D
Overall, this is awesome! =D
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CA