After a library has been created with the "Copy items to the iPhoto library" option unselected, can it later be made to create those copies?

iPhoto 9.4.3

iPhoto Library Manager 3.6.8

MacBook Pro - OS X 10.7.5.

I have a large number of iPhoto libraries, organized with iPhoto Library Manager, that I created with the "Copy items to the iPhoto library" option unselected because I wanted easier access to the individual files. I am now going to be migrating to a new computer and have run into some problems with iPhoto losing the path to the file, and as a result showing me the exclamation point of doom. What's more, the program doesn't seem very intelligent about rebuilding those lost connections, and I have to go back through and correct it manually almost one at a time. How do I get around this problem?

If I rebuild my new computer from a Time Machine backup (I usually enjoy taking this opportunity to start from a clean slate, but...), will the paths all be preserved without me needing to abandon my organization system?

Or is there some way to ask iPhoto or Library Manager to create and organize copies of all the photos in the library that are not currently present within the library?

On a tangentially related note, what's the best way to save keywords (and ideally also faces) added in iPhoto to the photos' meta data?

Much obliged.