OKAY. I played it right from the start, so I'll go from there.
WARNING: LOTS OF SPOILERS, READ AT YOUR OWN RISK
-Oh no, my gun ;_; Hopefully we get that back later... Anyway, the new Outer Wall part is nifty, especially with what you did to the Gunfish. I wouldn't say it was -really- difficult, since you can afford to take a hit, but it can get pretty frustrating, and not everybody has had months of jumping practice in this game like I have. I did get it eventually, but maybe removing just a couple or (God forbid) adding in another save point would make it slightly friendlier.
-Bye bye Missile Launcher, HELLO SNAKE! (Or Shurukin, as the case may be, I'm not sure. It says "you got the =Snake=" when you open the chest). Either way, it makes you a lot more versatile than before. The Pump Room boss is still really hard (I cheated lol), but you said you'd be making it easier, so I guess that can wait.
-Made it through the aquaduct okay, and... POOF. RESERVOIR, YAY! I like how you set up the Mimiga Villiage, especially with the teleporter door thingies, although it can be hard to naviagte in places, which seems odd for a 'safety' zone. Not everywhere needs to have tricky jumps and the like.

It's also a bit odd that the Map System is in the exact same place it was before. And a couple of debugging things: on door events #115 and #118, you can still move after you open the door, and on returning from the Mimiga Tower the door doesn't 'open'.
-Just a more of an aesthetic issue conserning conversations. It looks a bit weird with Julian's face popping in and out when you talk to people, and it's not like you -have- to have him talking to everyone. Maybe you could have one serious conversation with someone who actually has a face image (meaning Jack or... Jack), and then talk 'normally' with everyone else. That is unless you want to make face images for everyone, and somehow I doubt you do x.x There are also a couple of errors in the conversations you have with Chaco.
-Speaking of Chaco, SHE HAS A SON?

When did that happen... anyway, I'm guessing you have yet to edit Oscar's sprite, otherwise he looks like the little girl from the original ._. Oh well, DOWN THE CHUTE WE GO.
-I can't help but wonder why nothing has come out through the other way yet... anyway. How the heck are you supposed to get past the moving block and spikes at 34, 4? I couldn't get through without getting snapped at the edge, I had to turn on invicibility to get past it (THANKYOU Abu's Trainer). Even getting hit by the Gaudi doesn't help since there simply isn't enough space to get through. And in the second part, the spikes at 7, 8 are just unnecessary, I can't seem to jump without hitting them (and consequently dying). Maybe if you move them up one square...? Apart from that, the levels are perfectly beatable and actually well-designed, though you could lay up on the spikes a bit in the second.
-OH NO WHERE DID THE LIGHTS GO. It's pretty clear you need to use the map system in here, but with only 10 health and 5 damage per hit you can be in trouble reeaal quick. Adding in a save point before you enter might make it less daunting, because it's really not too hard just to use the Map and spam the fire button constantly. It's certainly a new twist to the game though, so I commend you for that.
-Pooh Black... literally. I'm glad you put in a save point and terminal just before it, and luckily I still had God-mode on (muahahahahah... I'm lazy

). The trouble is it's very hard not to get hit when he comes flying in, especially when you can't see where you're going, and again you only have 10 health. Maybe by making that +2 capsule early on a +3 would making things a bit easier, since with 11 health you can take an extra hit. Anyway, he dies, and... LIGHT. OH THANK GOD. At least getting back is quite a bit easier than going forward (except for that blasted moving block). And the critters are yellow <3. I assume you aren't meant to get that Health Capsule yet, since you can't jump high enough.
-Aaaaand that's the end of it. Overall, it's a very good job, particularly with the sprite editing and overall ingenuity. As I've said, It could use some tweaking, but that's what the debug is for, right?

The only other qualm I have with the game is its lack of interactivity. In the Mimiga Villiage, for instance, barely anybody tells you anything useful, two say the same thing, and you are given no clues about where to go next or how you are meant to find the Ancient Tunnels, other than a gaping hole in the floor of someone's house. But it's a good mod for the most part; you've obviously put in a lot of effort, and I hope you continue with it until its end.