What is the best practice to index remaining content with solr?
The Apache Solr configuration page (/admin/config/search/apachesolr) provides a button under actions to index all queued content, which should send everything left in the queue. That can put a great deal of load on your server, so you should only use that option with some thought about how/if it will effect your users.

When I did a large import recently I went ahead and pushed it all the Solr as quickly as possible, but I was able to do that before the site went live. That meant that when users arrived the search index was complete.  If I'd had to do it while it was in production I would have spread it out to make sure the server was very responsive when they first started to use it.

The load that comes from extra cron runs is site specific. Some sites you can't really see the effects other sites it can have a noticeable slowdown from cron runs. I have worked with sites with light cron loads (or powerful servers) that run cron once a minute to allow functions like the Solr index or external data syncs stay very close to current. The 'right' answer here depends on your site, your server, and your users.

Also remember that you do not benefit from having cron run faster than it takes for an individual cron run to complete. If you have your Solr sync setup to send lots of large files for indexing in each pass it is possible your cron runs take more than two minutes.