Ragged right means you don't justify the text, so the right hand side has a wobbly margin. Often for columns they use justification, and for whole-page text they use ragged right margins as that's what's easier on the eye.
Gutter is the gap between columns and also the gap for where the paper is folded. Getting it wrong messes up the whole page.
You make colour separations for printing, one each for cyan, magenta, yellow and black. Nowadays it's a separate pdf for each colour, but in the old days it was separate photo-etched metal sheets or lithography stones. Lots of printers don't need you to supply it any more though, they just use software to do it automatically.
Off-stone is when it's all ready to print and it's too late to change anything. From the days when they used to use actual stone sheets in handtypesetting and lithography.
You make a dummy copy of the publication for everyone to look through to check before signing off. These days it's usually just simple computer printouts in plastic sleeves in a folder. So you can see what the real thing will look like and catch any last mistakes.
Em and en are measurements, mostly used for spaces and dashes. Em is the width of an m, and en the width of an en. Designers and copy editors get really fussy about improper use of em and en dashes. Lots of software like InDesign automatically corrects them to the right one now. Basically en-dashes are for inside words, and em-dashes as breaks in a sentence or to attribute quotes.
Morgue is the reference files.