You should be able to match the all caps stuff with a simple

/[A-Z]{2,}/
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for each piece of the name, where the curly bracket part means match 2 or more. Now for the whole name, try something like

/([A-Z]{2,})\s+([A-Z]{2,})/
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To generate the unique identifiers, I would just create them as you go along and store it in a hash so you can repeat. Something like this might work:

if (exists $ids{JON_DOE}) { # found it, use old
    s/JON DOE/$ids{JON_DOE};
} else { # create new
    $ids{JON_DOE} = "UNIQUEID_$i";
    $i++;
}
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Updated: regex for whole name