I'll try using the debugging, thanks!
The http://www.gamesas.com/topic/1345130-having-papyrus-trouble-here-are-some-things-to-try/to the top of this forum has good information about how to enable debugging and such. Without knowing specifics of your quest it's difficult to suggest what exactly to test for, but often folks try displaying debug messages when a quest starts, a message with the contents of any reference alias if you're using them, you may be able to test in Papyrus for any relevant dialogue conditions and spit out a message if they are true or false, etc.
What is hard-coding form id's based on a mod's load order? I don't know if I have done that.
Basically don't ever use Game.GetForm() to get content created by your own mod.
What really irritates me is how the files are all spread out in creation kit, and not very well named - I have to name them all myself (like the fragments), but if I forget for one, it's very easy to lose it. I wish there was an easier way to pack my mod - I never did the archiver. Maybe I should try that just to see if it helps at all.
In File > Preferences > Scripts you can define a "prefix" that all your fragments will be given (well, all the ones after you define the prefix; you'll need to regenerate the existing fragments if you want them to have the prefix, too). You can then sort the scripts directory by filename to group your scripts together (assuming you use the same prefix on any scripts you create by hand).
The archiver built into the CK is a mess, it often doesn't include necessary files. There is also an http://www.creationkit.com/Archive.exe that does a better job.