1) I'd say just use an x-acto knife, or if you're used to it, ripping out the pages/tearing the entire issue down the middle is safe enough.
2) You can't do hand-sewn with single pages, but glued and oversewn work the same as if the issues were mint
3) It's case-by-case. I leave in the cover only if it relates to the pages I took out. For example, I included excerpts from 52 #30 and #47 at the beginning of my bind of Morrison's Batman run, but I only used the cover of 30 since it was Batman-centric.

edit: bluedevil beat me to it!