Settings ? Just re-do your personal setting. Applications ? Titanium will take care of that. Don't know if you've actually restored w/TB but once loaded with batch restore you can pick & chose which apps to restore, or just do them all. I have noticed that when restored w/TB my installed apps don't all show up in market, ie: for updates.
As far as the md5 mismatch, I've stopped changing my backup names and haven't had any problems since/so far. Also, on a couple forums, posters have noted that placing blank spaces between words sometimes gave them mismatches. Possibly was my problem. Use skennelly's suggestion & place "_"
instead of blank spaces.
I had a similar problem a few days ago. Created a backup that failed to recover. I was running ClockworkMod 184.108.40.206. What I did was Flashed ClockworkMod back to 220.127.116.11, created a backup, and immediately tried to restore it. It worked without a hitch. I triple checked it on my Thunderbolt, without a problem. My phone is rooted, running Thunderstick GENII 2.2.0.