Finally finished the new version, and compiled a list of bugs. A lot of them I've seen reported already, but I'll mention them again, just in case (repeated bugs marked with *s).
It's still possible to get to the Revolutionarium early (lure the jumping guy over and bounce off him). Same with that life capsule.
Refill station in the "Familiar Cave?" only says "Health refilled", even while you have the Snake.
Door from First Cave to Mimiga Village: Door sound with no door.
Door from Chimney to Yamashita Farm: Door, but no door sound, door doesn't open.
*Can get to Egg Corridor without Air Tank (is that supposed to be possible?)
*Grasstown: "Max missiles increased by 5" message.
Sand Zone: Not technically a "glitch," but if you kill the Deconstructor quickly enough, there might be a ton of the little things flying around still, and the long wait period after closing the message window means you might get hit (which you wouldn't be able to do anything about). Suggestion: destroy the little things when the Deconstructor dies.
Hermit Gunsmith: Check empty treasure chest, and it makes text sound twice (once before text appears).
*Labrynth Shop: Checking computer after getting back to Mimiga Village and getting the Air Tank gives same message (Curly shouldn't be surprised you're alive, at least, since she's already seen you). Also, checking a second time, Sue still tells you to bring an address chip, even if you already have brought it.
Door from Chimney to Disused Room: No door sound/opening door.
*Mimiga Village: +5 missle chest just underneath exit from First Cave reverts to "closed chest" sprite (although it's still empty).
*Egg Corridor Storage Room: Lower entrance door takes you to 2 spaces too low?
*Grasstown: After completing the Labrynth, you can get back to the Construction Site (which was supposed to have collapsed). Entering it then leaving again drops you into Genesis: Sky. This was after I'd already fought Genesis. Further, continuing to the end of Sky, then Earth, the only exit (that I know about) leaves you stuck in the wall in the Sand Zone.
*Genesis: Can collect the Address Chip multiple times.
*Oblivion: It's possible to get there.
Also, three more that I apparently had seperated for some reason. Might not have checked them in this version, I don't know.
Sand Zone - Jumping bone-thrower guy near Small Shelter (upper right) falls through sun blocks
Sand Zone - Bird and Skull at beginning of secret Gaudi teleport (on the way to Misery's house, I think) doesn't have enough room, skull stops at ground while bird keeps going down.
Labrynth - Dead End exit goes to wrong door?
Like many have said before, awesome mod. XP Can't wait to see it finished.