Will have a little play about with it later today and report back with my feedback. As you suggested, I will only apply the code-changes to the 6 files that had code conflicts and let the automatic updater do the rest.
Have just applied the changes using the auto update package and replaced any files that conflicted.
Only file I had trouble with was functions.php which turned out to be easier replaced with the new one and then I added the MODs back into it.
Output file was generally easy to follow but noticed that it picked up a few spacing differences as changes.
It also uses FIND } a lot which is confusing but is always referring to the } right after the last edit.