Why does my 2009 grand marquis idle rough?

Recheck your work, sounds like a vacuum leak.

WHy did you replace the intake ? ?

Don't you just love pseudo-mechanics? Is the manifold right for the engine? Is something loose, like injectors or vacuum lines? Did you break something in the process? Enquiring minds wanna to know!

Did you scrape down the surfaces for the new gasket? Bet there's a leak. Re-do the job, squirt gas around the intake joints, and see what happens. (just a little)