Although it is possible to use the diff files to manually upgrade a file, it may be faster/easier/less stressful to use a text editor with a "find differences" feature - and compare your existing file to the BRAND NEW virgin 4.1.8 from the distributive.
WHAT I DO when I have a small list of files that must be manually upgraded:
1. backup, backup backup. I even make a tarball just to freeze the moment.
2. assemble the list of files that must be manually patched
3. manually open the "old" file vs the new - and do a compare. choose which code blocks you want vs. don't want. or in the case of mods, your "old" file should be well commented, so you can EASILY see what is needed.
Last upgrade I did this to 25 or so files in 10 minutes. It doesn't take long, as some files may only have a line or 3 that are different.
This method requires some knowledge of your code and you should be able to look at a file and understand why some code belongs or doesn't belong.
My text editor does a very good job of comparing files and it has a 3rd window with the differences (on a per-line basis) and a button to "merge" or copy data from old to new, or vice versa. It is very elegant.
http://www.barebones.com/products/textwrangler/
You'll see that the xcart upgrade script sometimes misses, and your "old" file may be identical in every way (excapt maybe the timestamp header) - so in this case, I just copy the new file over. You just have to be smart about this.