1) removing intros isn't that easy. Sometimes, you just won't be able to do that (unless, of course, you disassemble 1st_read.bin and recompile it...). You can find other posts about this subject on this forum. Look around.
http://www.fileforums.com/showthread...t=remove+intro
http://www.fileforums.com/showthread...t=remove+intro
(for example...)
2) it's just your CD's label. You can change it easily, by specifying another label before burning your CD. You might be able to change it with CDMage (not sure). Otherwise, extract all files and remake an ISO with your favorite burning tool.
3) I do that all the way, simply because I make modifications quite often (downsampling, changing images or sound, ...). As far as you binhack correctly 1st read file, it's ok.
4) Use any format you want. Data/Data should be supported by newer DCs. It's the one of the differences. Data/Data format also takes less space, so you might save some space (for selfboot purpose for example) using this one.