A bootable clone is an excellent idea. Here is the strategy I use now after having some time machine issues and spotlight indexing issues.
pre stats:
Internal HD 1TB, 100GB used
External FW HD 1TB, formatted as 1TB backup
External USB HD 320GB, formatted as 320 GB exfat (this was just a movable drive I use between my work/home, it does not stay connected)
Key programs I have...Disk Warrior, Carbon Copy Cloner, clean my mac
I cleaned my internal HD of trash, caches, etc using a program called clean my mac. I turned my time machine off. I then reformatted my backup drive creating two partitions, one I could boot from and fix things and one for time machine. I then reformatted my USB drive as something I could boot from and space so I can still use it to move stuff between work and home.
post stats:
Internal HD 1TB, 100GB used
External FW HD 1TB, formatted at 880 GB backup and 120GB emergency
External USB HD 320GB, formatted as 200 GB exfat and 120GB emergency
Disk utility was used to change the disk formats.
I used Carbon Copy Cloner to clone my internal HD to the emergency partition of the FW 1TB drive. I also used the same program to clone to the emergency partition of the 320GB smaller USB drive. I ran disk warrior on both clones and it found errors on both in the directory structure. I allowed it to fix those errors and then ran the files/permissions check.
The next thing I did was turn off spotlight indexing of my internal drive by adding the drive to the spotlight exceptions control panel. This will delete the current index.
I validated by clones by booting from them. Satisfied that they worked, I turned my attention to my internal HD and ran disk warrior on it (you can only do this if you boot from a clone drive). It also found directory errors which makes sense considering it found those errors on the clones. With my internal HD fixed and files/permissions checked, I rebooted using the internal drive.
I now turned spotlight back on and allowed it time to rebuild the index, when it was done, I turned time machine back on selecting the 880GB backup partition of the FW drive.
So I ended up with two bootable clones (one as backup to the other), a clean and error free internal HD, a new spotlight index based on a correct file structure, and a new backup that works as it should. If I lose my internal drive, my external FW drive can get me back and running. If I lose my external FW drive, I still have my portable as backup to my internal.
My strategy may not be the best but it works for me. The most important thing in my opinion is to have an ability to boot from a clone to address any issue that may affect your internal drive.