How To Update Post Indexer from Legacy Version

I'm hoping Andrew or another lead developer well versed with the Post Indexer plugin can provide some recommendations for updating from v.2.1 to v.3.0.5.7 and Recent Posts from v.1.0.1 to Recent Network Posts v. 3.0

To make a long story short, due to various issues we encountered and an unresolved support topic long ago when updating Post Indexer on our dev site, we never updated it on our live site.

Recently, however, our Blogs Directory page started throwing an Invalid Page error, likely due to the WP 4.0 update and legacy Indexer.

So... by skipping so many versions, I'm thinking it may be best to completely remove all Post Indexer related db tables. Right? No?

It looks like the plugin v.2.1 created the following tables:
wp_term_counts
wp_site_posts
wp_site_terms
wp_site_term_relationships

But I notice our db also includes:
wp_sitecategories
wp_sitemeta
wp_site_comments

Is it recommended to remove these tables before updating? If so, which ones? Any other data in other tables I need to clean up? Is this even necessary?

We have 1000± sites on the network, so I'm just very concerned about downtime and/or Recent Posts not displaying due to any update glitches or re-indexing.

Thanks in advance for any suggestions!