Unfortunatelly I can't help you with the modules but I hope it will not be abandoned, it's a great tool that just needs to be refined in some aspects.
Besides from the designer error with apedelta.swc ( I assume this is a common one) I get a crash when closing Flashbuilder, until now no other errors but I have noticed that working with large files ( more than 4.000 lines) becomes very slow.
Also it's important to clean the project sometimes or you will start to get non expected errors.
Many of the problems I had could be solved by creating a new simple testing extension and working only with this problem or feature I want to introduce.
I would suggest you to drop Flash Builder 4.6 (which is a real pain in any delicate part of the body you'd like to pick) and stick to version 4.5 - there Design mode is not flawless but magnitude orders more stable. This of course if you don't need 4.6 features for other projects.
As for the rest I'm not in the position to give you answers.