You shouldn't use a debugger to search for differences. You should use a diff tool. Of course, most diff tools work on ASCII text, but there are some that deal with binary files.
Some examples:
There are more and you probably will find one that matches exactly your need.
If you would like to see your modifications in a nice visual manner with already bytes being presented as opcodes there are some options too. I haven't used them (so can't give you my recommendations) but there are at least two that I know of: