Bad habits... lots of them^^
I dont want to be rude there, but people are generally more likely to help you on the internet if you describe your problems and concerns at least a bit readable.
Punctuation is important
Pressing enter from time to time is important, too^^
It's just pain to read a long text without punctuation or passages... most people dont bother with it.
However, since i dont want to play the stereotypic grammar nazi, now to your topic:
first, i never really bothered with flour, but as far as i remember there are reactions to make bread out of it in the masterwork mod... or even vanilla?
i guess the mod, but meph can tell you, i guess.
second, you dont have to bother with your manager, setting up butchering commands.
your dwarves wont butcher anything that isnt in your stockpile. (with the exception of tame animals, ofc)
so what you want to do is o:set orders and options r:refuse orders o:accept outside refuse(or something like that)
problem solved
third, was he a soldier? not sure if they use magic as a civilian, too.
however, you have to be careful with mages, especially the firey one.
use burrows for him... let him train with a few other soldiers deep in your fortress to have a little elite if everything else fails.
make your fortress easier to defend.. so you can be 100% sure no sneaking units can simply go in as they want to.
thats a general tip, however, not something thats only important with mages.