Troubleshooting Slow Craft Website - New Relic
I don't know where the first set of data you posted is coming from, but in the attached stack trace autoloading is only .54% of the total request.

Whatever template(s) you're rendering account for 65% of the request (for a total of 8 seconds), so I'd start inspecting there.

Loading all of the plugins you have installed is about 10% (which accounts for about 1.3 seconds of the request), so I'd investigate those as well.