The Map System gets destroyed by the Doctor without telling why, ZarroTsu should include a message after you picked up Quote's items (If he had the Map System. The message is skipped if he doesn't). By the way, you can get another from Itoh in the Rest Room at Plantation. The Air Tank problem is already fixed, please download 1.1.0.0 (or later) at the first post.
The Helicopter bug is already reported by me, please check post
#58.
Defeating Monster X is possible and you get the Catseye Medal item. Whether or not ZarroTsu wants the boss lifebar is up to ZarroTsu.
The Save Point placements is up to ZarroTsu.
Maybe the Pignon must be CNP'd (twice?) to the same Blue Pignon to replenish health? Also, ZarroTsu would have to put a new skipflag and rearrange the text to display three lines at a time before CLR to allow speed through text.
The trading-back weapons is up to ZarroTsu. If you really want to keep the Machine Gun, simply say no. This trade is final if Yes and you get the Fireball.
The areas where the ingredients are located are found in the bookshelf at Mimiga Tower (a Save Point, next to the chest) in Mimiga Village. For the five prior, expect a reply in PM by ZarroTsu or wait for the walkthrough. In Devil's Garden, it's intended to be very difficult, but I'll give you a hint. Follow the doors with the skull lit up red, then through the possessed doors. In the maze, the left with skulls is the first path, so go left, right (where you came out of), down, right and then up. Then go up and open a chest if you still have the Snake, go through the door at the bottom where you came out of. You'll wind up back where you started, however the door ahead will take you to Hell.
How Curly got there before you... Sue finally got the Observatory teleporter working remotely from the Town Hall's computer by decrypting a code somehow while you are going through either the Egg Corridor and Outer Wall or Devil's Garden and Hell. Curly traveled by teleporter as the shortcut and told you why.
The bosses, leave it up to ZarroTsu.