I apologize for not reading the whole thread; if the answer is in it, I am truly sorry.
And the question: I saw there is an installer for the February the 8th release of BBClean 1.16: bbcleansetup0802.exe

The thing is, I have done some customizations to my BBClean setup, and wuld hate to lose them. Is there any way for me to upgrade to the new release without losing my own changes? If not, what would be the safest way to do this upgrade? I don't anymore remember which files I edited.

IMHO safest way would be:
1. Backup your whole bb folder.
2. Try to unpack the installer (with 7-Zip for example) somewhere.

If succesfull:
a3. Only overwrite old binaries (exe's and dll's) with new ones.

If unsuccesfull:
b3. Install the new version.
b4. Overwrite all settings files with the old ones from backup.