Normally the cowl (technically cowl cover) is that part between the base of the windshield and the hood, but on a 97 Accord, its the black piece under the hood at the base of the windshield.
On the drivers side, you can see through the vent holes in the cowl cover, the wiper motor is under this side. This lets the air into the cowl, the vent to the cabin is under the solid section on the passenger side. You have to remove the wipers, then the six plastic anchors with the phillips head in the center to remove the cover.
As for removing the doors in the vents, I wouldn't do that. If you leave the vent on inside air all the time, then the mice should not have been able to get into the blower motor area, but there might be a dead mouse on top of the vent door, or a mouse nest on top of it and baby mouse urine or the smell of the dead mouse is getting down into the blower compartment. When they take out the blower motor, the need to open this vent door to see.
BTW, it doesn't matter whether your on inside air or not, some outside air, with all it pollutants (and fresh oxygen) get in anyway, just not as fast.