Why don't you just use rsync? This is a significant undertaking when the wheel has already been invented.

Yeah .. look at the rsync source for ideas

Ok well build a file index of your source directories and destination directories. Then build a list of source/dest files that do not exist in either folders and delete/add them as necessary. For files that do exist in both directories you should use an md5sum and filesize check depending on how careful you want to be. Collision rates are very low (unless malicious and intentional) for md5sums so you could probably get away with just do that.

You could use ls and parse the columns, or use du or stat :

bash Syntax (Toggle Plain Text)

root@svn:/root/backup# du -b backup.sh | sed 's/\([0-9]*\)\(.*\)/\1/'
4252

root@svn:/root/backup# du -b backup.sh | sed 's/\([0-9]*\)\(.*\)/\1/' 4252

Just because the size is the same doesn't mean that it has not changed so also compare the md5 stamp:

bash Syntax (Toggle Plain Text)

root@svn:/root/backup# md5sum backup.sh  | sed 's/\([a-Z0-9]*\)\(.*\)/\1/'
241cca25e509409c1fbd6f1d46ec94e6

root@svn:/root/backup# md5sum backup.sh | sed 's/\([a-Z0-9]*\)\(.*\)/\1/' 241cca25e509409c1fbd6f1d46ec94e6

Now just automate all of that and you're good to go!

As far as your concept for builing the directories -- yes, that is how you would go about it. However ls prints out a lot of crap you don't need for this so you would be better off using find /src/dir -type d to make that directories with mkdir -p and then use find /src/dir -type f to get the files.