CPU usage goes up at specific time of day probably because of Mysql
100% CPU very often means one particular query is running.  And it needs a better index.  Or a better formulation.

Turn on the slowlog, with long_query_time = 1.  If you can get to the file, then use mysqldumpslow -s t or pt-query-digest to find the worst coupld of queries.  Then we can discuss what 'composite' index to add (or whatever).

Swapping is terrible for MySQL.  Lower some settings to avoid it.  Let's see my.cnf and RAM size to help advise.