I do not understand exactly what should be wrapped into groups (the beginning of the output is missing, anyway). To insert CDATA and change rid attributes, you can use XML::XSH2 in this way:

open 908451.xml ;
for $t in //title/text() insert cdata $t replace $t ;
for //article-ref/@rid
    insert text xsh:subst(., '.*-2_' , '') replace . ;
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The rest would be also possible if you can explain the algorithm.