Mine idles about the same. Mine whole truck shakes but that is from a bad engine mount. I need to replace. Hope that this helps.
I don't think its the motor mount.
My 3.0 does that too, but after I changed the fuel filter it ran smoother. before I did my engine swap, my truck idled at around 900 rpm. I need to bump it back up on the new(er) motor, and see how it works there. You said it had sat for a for months? The engine I put in my truck was from an 884runner that was parted out, and the motor sat for a while. It seems as if these 3.0s dont hold their running qwuality for very long when left unused 
Maybe I should check my fuel filter and see if it is dirty, also my throttle is sticking when I leave it sit for around an hour. I put oil on it but it doesn't help any.
