I have a page template which aggregates multiple CPT's in different areas of the page and displays the first post from each CPT. I'd like to add a separate pagination for each of them. Is it possible with or, preferably, without a plugin?
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Its possible! When i find myself in need of multiple paginations in a page i usually use ajax. take a look at this tutorial which with a little modification can do what you want.
If anyone is looking at this in 2020 and found that the link from Bainternet's answer is broken, here is a snapshot of the article on the Wayback Machine: https://web.archive.org/web/20110625064315/http://wordpressapi.com/2011/05/16/add-ajax-pagination-in-wordpress-blog