Slow MySQL query performance is all too common. Of course it is. A good way to go is, naturally, a dedicated profiler that actually understands the ins and outs of MySQL.
The Jet Profiler was built for MySQL only, so it can do things like real-time query performance, focus on most used tables or most frequent queries, quickly identify performance issues and basically help you optimize your queries.
Critically, it has very minimal impact on your server's performance, with most of the profiling work done separately - so it needs no server changes, agents or separate services.
Basically, you install the desktop application, connect to your MySQL server, hit the record button, and you'll have results within minutes: