After Mavericks reinstall, I copied iPhoto library over, but now photos missing?  Where are they hiding or how do I recover them?

I was told by Genius?Bar to reinstall Mavericks and avoid using Migration Assistant, but rather manually copy over my data because of ongoing issues.  I have a newer version of iPhoto now (9.5.1, not sure the previous version).  I copied the iPhoto Library from the Pictures folder of my Time Machine backup.  I want to keep all the folders, albums, keywords, etc.  Now, several photos are missing and showing an exclamation mark, however the folders they were in are still there.  I tried rebuilding the database and had no luck with that.  I still have the Time Machine back up, but no idea where the missing photos are if they aren't in the iPhoto Library file. Most of the photos were imported from an iPhone and iPad, so not sure if there is a default location they would save to other than iPhoto Library?  Any help is greatly appreciated.

but the Genius Bar guy specifically advised me to "drag and drop" my data
That will not work - TM backups MUST be restored - not copied - seehttp://support.apple.com/kb/HT1427?viewlocale=en_US&locale=en_US andhttp://pondini.org/TM/FAQ.html
There is nothing more to say - it will not work and you have proven that to yourself by doing it and having it not work
LN

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