Sputtering at idle

Friend of mine bought this car as is, it was very inexpensive. She was acting bad first as far as dash flashing and so forth we put a new battery all was good, but it kept having a check engine light on and a sputtering, rough idle at start up. Even when it's warm, same thing, but only at idle. If you rev it up smooth as silk, if you drive it, very very smooth.
Code was for the thermostat heater element, mapping thermostat I believe. Replaced it and code was gone. Still sputtering. Had misfire on 1 and 3. Checked hoses and found the bottom PCV part underneath the intake was broken, replaced it and gotten better. Found another hose cracked along the PCV system, replaced it, gotten better. Found the plugs black, replaced them and coils as well. Kept getting diverter valve code, removed it and checked it with vacuum gauge and works fine, put it back, still getting misfire on 1, 3, sometimes 1, 2, 3. Checked the valves when I replaced all this stuff and they are very clean. Checked many vacuum hoses can't find one with a leak or a crack anywhere.