Migration assistant only partially copied my Mac's contents

So I did a clean install recently and I tried to use Migration Assistant to copy all my files over. Through Time Machine, Migration assistant only copied ~640 MB (mostly apps). I manually copied the rest of my user data from Time Machine.

Is there any way to either:
a) get Migration Assistant to actually copy everything from my computer pre-wipe
b) Use my Time Machine backup as if there was no re-install and just restore everything I had.

The two main issues I have with what is copied currently are:
1) various user settings were not copied. My Mac is now like it was out of the box software wise (for example, the default doc apps are in the doc)
2) Some applications such as MS Office no longer work. The have the generic "Application" icon in Finder and when I try to launch them, Finder says they "quit unexpectedly". iLife is messed up as well. Garageband is absent and iPhoto is corrupt.

Any help?

Weaselboy said:

Attach the TM drive then option key boot to it. When the recovery screen comes up use Disk Util to erase Macintosh HD to Mac OS Extended (Journaled) format. Then quit Disk Util and click restore and everything including the OS and all your data and apps will be put back where it was at the time of the last backup.

I'm going to guess you had trouble with Migration Assistant because you made and your user account after the fresh install then used Migration Assistant afterwards to import that same account. That makes a mess with duplicates. The way to do it is run Migration Assistant as part of the setup wizard at the end of the fresh install and not make an account at all.

Click to expand...

Thanks. Your guess is right on. I used migration assistant when I got my new computer ~2 years ago and it worked fine then.

This time, I did a manual drag and drop of all my apps and documents and my computer feels brand new (was having some graphics issues with scrolling, which is what led me to erase everything in the first place). I also freed up a significant amount of hard drive space and the whole computer is snappier. It's enough of a gain (and spending more time on this enough of a hassle at this point) that I'm going to leave it as is.

The only drawbacks are:
-old messages/conversations don't show in iMessage
-some software licenses did not carry over, thankfully all the essentials work
-My computer is now counted as a new device for all my iTunes content/apps (i.e. one of the 5 uses that you are allowed)

Any idea if I can fix any of the above?

As an interesting aside, I had to go way back to May 5, 2013 to find a correct backup of certain apps.