Tools -> Advisors -> Timing Optimization Advisor. It's really just the the settings already available under Assignments -> Settings, but organized to show the ones that help timing most of the time.
The big ones are having synthesis optimize for Speed and have Physical Synthesis on. That's 90% of the gain.
Go into TimeQuest and do Report Setup Summary(I assume it's a setup failure). Right click on the worst domain, Report Timing. Change the detail to Full Path and number of paths to 100. Then sit and look at the worst path that comes up. What's the setup relationship? Does that seem right? (It's based on the clocks you described). What about the clock skew? Is that correct? (If it's pretty small, say under +/300ps, then your clock is on a global. You can probably do report_timing with the -detail set to path_only, which just hides some of the clock details into a single number. THe slack is still the same). Finally, look at the data path under the Path tab(part of the Data Arrival). Try to figure out how that correlates to your logic, why it's so long, etc. By far, the best thing to do is to change your code to make the path smaller, but it's also one of the more difficult things to do and not always possible.