Yeah you are right enough about the blow holes, was planning on cutting them in the top of the speaker boxes, think about a 3" diameter on each should do it, I don't think the main case will need one for the sub though because of the two fans that will be running in there (that might just be trial and error though).
Regarding the too loud thing, funnily enough someone mentioned this to me last night...I think the best solution could be the simplest one, put an IR port on the front and setup winamp with that, then just use a remote to skip/increase volume/decrease volume/mute.