> I take it they're referring to the free RAM as listed by 'free' or 'top'?
Yeah, it is hard to really figure out how much RAM is available. "top" lists free memory and swapping. Swapping is a serious no-no. If you are not swapping and mysqld is running and there is still some "free" space, than think of that as how much you can increase key_buffer_pool and/or innodb_buffer_pool_size.
> The link that Peter gave me says to use 20% for *just* MyISAM and 70% for *just* InnoDB, but I use both as the situation dictates.
The link goes on to say "If you have a mixture of engines, lower both numbers." OK, that doesn't help enough.
I augmented that link for your case:
http://mysql.rjweb.org/doc.php/memory#another_algorithm
> I haven't created any tables since the upgrade, so I'm assuming that the switch to the default of InnoDB
Correct. Ditto for innodb_file_per_table.
> I also enabled it for queries that don't use indexes
I find that setting virtually useless; turn it off so you can find the real problems.
> long_query_time ... changed it to 1
Good.
When you spot the naughty queries in the slowlog, let's see a couple of them, together with
SHOW CREATE TABLE
SHOW TABLE STATUS
EXPLAIN SELECT...