I would normally have 2 instances of BC open - one to compare un-modified copies of 6.5 to 6.5.5 and another to compare 6.5.5 to my currently used files - those changes in the unmodified versions I would then hop over to the other instance and make the changes there.
You can't really stop with 6.5.4, as a couple more security holes were found by script kiddies that allowed them to upload shell scripts and take over servers - hence 6.5.5
Your problem is gonna be that most files were changed going from 6.5 to 6.5.5, will take you hours to get them all in. If it were me I'd move straight to 7.1.1 and forget trying to save those little bits and pieces. An hour of template work and you can make 7.1.1 look an awful lot like what you are running now.
