1. IsoBuster work great or you can mount the bin with CloneCD virtual CD (included with the lastest version of CloneCD). and copy the files out (will not work with hidden files).
2. it is possible for extracted files to take more space then the bin file due to block size of the hard drive. total blocks used to store multiple files may be bigger then total blocks need to store one file due to unused space in block. files are pack more closely in bin.
3. you can use ps2cdgen to create a cue/bin from the files in the HD. you don't need to convert from ISO to BIN
4. BIN file you created should be the same size as the original BIN, if not, you are doing somthing wrong.
5. patch usually apply to cue/bin file with ppf-o-matic
6. I agree with ThAD0oD, you could have ask all three questions in one thread since they are all related.
PS2: NTSC 39001 V7 + Messiah 2