If it were me I would leave the plugs out forever. As long as you can get the temperature stable that is all that matters. Embryos need fresh air at all times during incubation.
Added- you don't have to have a fan but fans make the air in the incubator the same temp. were as no fan you would have hot/cold spots, which could drag out the hatch or affect the overall hatchability of the eggs. If you are missing the window I would use a piece of plexi glass.
I install the plugs off and on if I need to raise the humidity a little but have at least one of them out most the time, both are out at hatch. If the window is missing it just needs glass or something glued or taped over the opening. Fans equalize the temperature in the incubator so you don't have so many hot and cold spots, the general thinking is the fan models are a little more sucessfull
100F is working well for me, I am using a part time fan, it is on when the heat is on. With a digital controller, the heating element and fan cycles pretty often so there isn't a lot of temperature difference from corners to middle or top to bottom.
Normally 99.5 for incubators with fan and 100.5-101 for still air are recommended for incubation.