Lost some of my photos after upgrading, though I can still see the previews.

My 2.66 intel core i5 IMAC recently had a HD crash.  Fortuneatly I had a 2T western external HD set up as a time machine.  The local Apple reseller checked the HD and had it replaced.  When I got my PC back I noticed it had the newer operating system and the newer ilife 11. I attached the time machine and began a restore.  All seemed to go well.  When I opened iPhoto for the first time, I was prompted to have the library upgraded for the newer software which I did.  Then when I went into iPhoto to check my pics.  Everything seemed ok until I opened my last import to see that even though I could preview all my pics, I could only open about 20 percent of them.  The rest displayed a large grey exclamation point.  What has happened and how can I recover these pics?  I am now thinking I should keep raw copies of all my photos (have about 40,000), is there a way to export all the raw pics from iphoto without doing each one seperately?
Been a big Apple fan for many years and trying not to let this change my opinion.

Try all options except for the thumbnails.  If that fails:
Using iPhoto Library Manager  to Rebuild Your iPhoto Library
Download iPhoto Library Manager and launch.
Click on the Add Library button,                         
navigate to your Home/Pictures folder and select your iPhoto Library folder.
Now that the library is listed in the left hand pane of iPLM, click on your library and go to the Library ➙ Rebuild Library menu option             
In the next  window name the new library and select the location you want it to be placed.
Click on the Create button.
Note 1: This creates a new library based on the LIbraryData.xml file in the library and will recover Events, Albums, keywords, titles and comments. However, books, calendars, cards and slideshows will be lost.
Note 2:  your current library will be left untouched for further attempts at a fix if so desired.
OT

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