Compare custom taxonomies of updated post (or new post) [Updated with progress]

Use the set_object_terms hook,

http://adambrown.info/p/wp_hooks/hook/set_object_terms?version=3.4&file=wp-includes/taxonomy.php

It should be fired when a post or page is modified.

Here is the code that fires it:

do_action('set_object_terms', $object_id, $terms, $tt_ids, $taxonomy, $append, $old_tt_ids);

You can thus check against the $object_id and taxonomy, and flush your transient cache and regenerate as needed.

Specifically, clear the term caches of the term IDs in $tt_ids and $old_tt_ids