You need to get yourself to the busconversionmagazine.com site/forum. They are Coach folks and can help you. Here they mostly know school buses and such, with a few having some Coach experience. I have lots of Coach experience and watch both forums.
For your quick information you should know that the air inlets in the floor ramp area are for the intake of internal coach air down into the re-circulation and fan plenum chamber under the floor and in front of the forward baggage bay. There are removable service panels were you can reach and service the fan motor and the heater core and A/C evaporator core too. The air is forced from there up into ducts just under the floor running front to back at the outside walls on both side under the windows. These ducts have risers that carry the cold air up and out of the registers at the bottom of the window frames. It's obvious that these risers have been removed and only the holes remain leading into the underfloor cooling ducts.
The internal air is sucked into the vents at floor level in the ramp area and returned under pressure from the sidewall ductworks to the bottom of the window outlets. The intent is to create an internal cold air flow that rises up along the sidewalls and is deflected by the parcel racks to swirl around the passengers and eventually be sucked back in at floor level to be done again.
A percentage of outside fresh air is mixed in to keep the internal air fresh and oxygenated. You can see the small vents in the outside skin near the A/C plenum chamber location where the outside air is sucked in.
If you are truly demolishing the A/C system and have no interest in using any of it's components you could cover the floor intake/return vents, as well as the cold air registers. BUT, if you have any ideas of using the remaining bus heater core and engine heat sourced heater capability, you're going to have to keep all these vents open and functioning. The air flow and fan that powers it is used for both internal Heat as well as A/C air flow.
I would STRONGLY suggest that you not destroy the heater capability since you will no doubt need it, as it also provides heat for the windshield defrosters. Even though they have a smaller heater core and fans in the dash area, the overall hot water plumbing from the engine uses the same pipes for coach heat as well as the front, drivers heater and defroster. Be very careful and don't demolish and remove something critical to the safe operation of your Coach. There's also a small A/C evaporator in the dash for the driver to cool him from the massive heat coming in the windshield glass. This is also plumbed into the Freon lines used by the main A/C system. It will need to be dealt with responsibly.
A word to the wise. Tread carefully and go slow. You WILL need the Coach systems, even though you may not think so now. Many have taken out the coach systems only to find out later the full consequences of their rash actions. Sometimes it's not pretty at all. Once removed it's terribly difficult to restore or put them back....