As long as you have your plugins in /my-plugins/ and your template folders in /my-templates/ then you should be able to go and just overwrite the files from the download into your bbPress folder. The download files don’t have the things you need to protect:
As long as all your changed files are in the folders, you can go ahead and upload!
I don’t know if I fully understand. You have your own template in /my-templates/kakumei2/ and that is all you should have to do. If that is your ‘bug free’ version of default theme, then you don’t have to copy over the default theme to /my-templates/ as it is the constant one that changes (hopefully bug free) into /bb-templates/kakumei/ and you shouldn’t worry about that one. Just the templates that you work on or change in your /my-templates/ directory.
I noticed there are a lot of changes to the default theme in this security update. My custom theme was heavily based on the default; will I somehow have to locate and propagate these changes to my custom theme? Or were the changes merely cosmetic?
diff is your friend to find the differences. You might want to diff the original and your modified version, then once you see what you changed, diff the .8.1 files with the originals and see what changed there. Then you’ll need to reconcile all the changes.
This is the sort of thing that prompted me to ask about using svn to take care of the changes.