You'll never get a consistently smooth idle out of the 1ZZ-FE, they idled like crap even when they were new. NVH has never been its strong suit.
+1 on andrewclaus' suggestions. I'd also add a caution to not cheap out on engine mounts if you are replacing them. Find OEM if you can, otherwise there's a chance the new mounts could actually make it worse and you'll be redoing the job. Ask me how I know.