||I'm converting a Thomas Transit and have done a bunch of reading on window removal and covering. I did a bus over many years ago and used marine plywood. While easy and durable enough, I didn't like the look of wood. This time around I'm using galvanized sheet steel.
Here's my two cents on what should be considered or adopted in your approach. Thickness should match the material your bus currently uses. Remember that some metals will react when put together through galvanic action. Don't put standard aluminum and steel together without some type of protection for instance. After window removal you will want to rivet the sheet metal to the existing structure left intact, usually some type of steel members. You should research rivets and use what closely resembles your factory rivet. As some bus companies use a hammered rivet which requires special tools, I would try to find one close, but allowing a pull-through shank design. Shavehead rivets look like a hammerd rivet, but are of the pull through shank design for instance. One tip I read is to be sure that the new sheet metal is warmer, or at least the same temp, as the bus. This means it will not buckle during expansion after applied. The rest is pretty much common sense - a lot of drilling and riveting. I would recommend riveting the extreme corners of the sheet first so as to keep the sheet flat and then do the middle. After that keep drilling and riveting the middle of what's left in sections until your done. Again, this keeps any buckles from being bunched up into a big mess.
Finally, common sense says to work from the back of the bus forward. This means the overlap is not exposed to front debris assault. When all the exterior is covered, it is a good idea to insulate and cover the interior. I'm probably going to try a spray foam that is then shaved to flat with the structural members. Then comes the fun of cutting in the new windows, etc. Hope this helps.