I took a brief look at some of your code - note that this is not a thorough code review. I'll just dump what I found here:
Plural.txt
-SetPlayerRebirthLossFrame() is usually used in Player Scripts, and is generally not done in single/plural/stage scripts.
-CloseStgScene() is generally not used in Plural Scripts. If you had placed it anywhere other than the very last line of execution, things may have gone horribly wrong (then again, don't know, don't exactly need to know).
-SetCommonData("scene",obj); - Get rid of this. You can get the boss scene using a function - GetEnemyBossSceneObjectID();
-Your #Background script #Background["./system/Background_Stars.txt"] does not exist
Resources.txt
-SetScore, etc. confuse the heck out of me. I have no idea what you're trying to do.
Start.dnh
-You run ObjSound_Load(music,CSD ~ "./bgm.ogg") outside of a routine. Since loading the resource should be blocking, I suggest placing the loading in a routine, preferably @Loading.
-You register new boss objects twice in the same script - once in @Initialize and once in @MainLoop at frame 0. Given that you are only supposed to be able to have one in existence at any given time, this may cause problems (then again, never tested so don't know the repercussions, if there are any to begin with)
-Your entire frame = 0 block makes no sense given that @Initialize runs immediately before the first run of @MainLoop. DRY - Don't Repeat Yourself
-Honestly, just terminate the script when the frame >= 90 instead of doing a workaround of using the boss's health.
-Your @MainLoop is not yielded. Literally everything in this script will crash and burn.
In general:
-None of your wait scripts are properly yield;ed so all of them will suffer from the same problems as the Start script.
-In all of your attack singles, your including of Resources.txt followed by blatant DRY violation with the definition of the same functions over and over again in your MainLoops worries me. Functions are limited by scope, but if you are using the same functions over and over again, just put them in your function library once and include the library. This will make your code cleaner and easier to read.
-Your redeclaration of the global constants cx and cy as local variables everywhere in your code only impedes readability.
I'm not meaning to be harsh, but if you do some code cleanup, it will be MUCH easier to find the actual errors in your script. Since the wiki is down, I suggest looking at other starter scripts (scripts where it was the second or third time someone made a proper script) - these will provide a good reference without being too bogged down in custom systems. Choose ones that are simple in scope, like some of the former contest entries that scored in the upper two-thirds.
Hope this helps.