I know that feeling! I think I've spent something like 10 hours modding so far! I'm actually planning to use XC_Bags modified to increase enemy HP and decrease skill damage as done in Scales. I liked the changes you made to crafting (particularly with the enhanced tormented souls and additional recipes, as well as ways to craft Man-at-Arms and other scrolls) and am leery of broader scripting changes as done in Scales. Plus, I've seen reports of crafting being broken entirely in some cases when using Scales, which, however unlikely, is absolutely a limiting factor for me.
Hm, even XC_Bags contains scripting, although more Osiris scripting than character scripts, but okay.
The only problem with crafting in Scales, as I see it, is that Baardvark only included an external crafting file from somebody else and did not bother much too look into it.
I've looked into one 'Extended Crafting' file once, it might even have been the extension for Scales but I don't remember if it was.
Anyway, the problem of a couple of recipes not working was an error in the crafting recipe syntax. It still had the old syntax from D:OS Classic and not the new one of EE.
The error was a missing 'autoValue 0' or 'autoValue 1' at the end of the recipe line for a lot of recipes.
A correct line looks like this
use category Oven on object XC_LOOT_Scraps_Wood_A_Mush with transform code Transform2 parameters XC_BOOK_Paper_Sheet_A,0,0,0,0,0,1,1 autolevel 0 autoValue 0
while the file I looked at had (look at the line endings)
use category Oven on object XC_LOOT_Scraps_Wood_A_Mush with transform code Transform2 parameters XC_BOOK_Paper_Sheet_A,0,0,0,0,0,1,1 autolevel 0
With the missing 'autoValue 0' at the end, the crafting engine would ignore the recipe line making the recipe 'broken'.
Easy fix.
(The recipe above is an exclusive from XC_Bags, you will not find it in other mods. The recipe itself is of no interest, only the syntax is interesting here.)
The biggest advantage XC_Bags has in crafting is that I only have new crafting recipe in my crafting files, I did not include the old ones. (But they still work)
A disadvantage for modders is that if they need a recipe overview, they have to look into two files and not only one ;-)
And I have a preview XML (ItemComboPreviews.lsx) which I think allows recipes to appear in the crafting window's 'Recipes' page.