I had a similar problem with my old truck, which I never really found a conclusive answer to. My 4runner however started running really rough at idle a couple of weeks ago, seemingly misfiring at idle badly. Once it revved passed about 1500 though it would smooth out, or at least I couldn't tell. I ended up putting some Heet in and my problem went away. My best guess is a combination of bad gas with letting it sit for a while with a low tank let moisture build up in the tank. I would kind of doubt that was your problem, but it is a cheap easy thing to try to rule out any gas quality/moisture issues.