Edit(2): Now using db-mysql with generic-pool module. The error rate has dropped significantly and hovers at 13% but the throughput is still around 100 req/
One thing to consider is the driver - performance to databases can be very tied into the specific driver you are using. The most popular mysql driver and the one that is the most actively maintained is https://github.com/felixge/node-mysql. Might get different results with that.
But if you are stuck at 100 connections, sounds like connections are not being properly closed. I might add a console.log statement in the pools destroy event to make sure it really is executing.