I would second the motion you consider a low floor transit instead of a school bus. Not only do they come with much higher headroom but most transit buses are 102" wide while all school buses are limited to 96" wide.
It is possible to lower the floor in places. I have seen where some people have successfully mounted a shower with the shower pan below floor level in order to get more headroom in the shower. But in order to do that you have to support the bottom of the shower somehow.
All school buses are built on parallel frame rails that go the length of the bus. On top of the frame rails stringers are mounted that go side to side. The floor is then mounted on top of the stringers.
Without even considering what might be mounted below the floor (fuel tank, air tanks, drive shaft, batteries, etc.) it would be impossible to lower the floor without figuring out how you would support the weight of the floor and everything on the floor. Regardless of how you supported the floor, the lowest you could go would be to the top of the frame rails. Lowering the frame rails between the axles would be a HUGE project and the result would most probably be not very safe.