Good points all.
generally infesations are not such a huge issue with bales, as straw doesn't have any real nutritional value it doesn't generally get infested, as say Hay might.
I'd probably render the inner surface and have the bottom section
(internally) done with sheets of plywood, this has proved sucessful before in an outdoor pursuits center to keep kids bags off the lime renders.
Windows are not a problem, you create a window buck ( 4 sides box) the same depth as the bales and insert it between timber supports, leaving a nice deep ledge for the birds to sun bathe in, it also hepls to stop rain penetrating as the ledge is ofetn 400-500mm deep.
Rendering with lime based mortars helps the building breathe all year, good sound properties so it's very peacefull and warm to boot.
Dense straw doesn't absorb as much water as youd think, and with decent overangs on the roof, much of the rain is kept off, except when it's driving at the building, endlessly for days and days and days...lol
The removeable poop tray will take a little engineering, can't you use a brush like all the rest of us???
The idea is to have a timber frame to keep all this together, so wall sections would be replacable should they get infested or damaged in any way.
I have done one for a sheep pen where we had to rebuild the shed after 5 years of sheeps wee had made one or two of the bales rot, but I think 5 years of sheeps pee would have that effect on many things, to get around it happening we lifted the bales up off the floor by making a 2 x 4 treated timber frame (ring beam), with a ply wood top, this did the trick and 8 years on, it's still in use.
Recycled car tyres can be used as the foundation blocks filled with hard pact hard core material, 2 tyres deep one or 2 high and a ring beam, you stagger the tyres so a line along the front and a second row inetween creating a triangular arrangement of three tyres, the tyres and hard core negae the need for a damp course of any type. I'lll have to get some sketches done and et you all see what I am thinking and then you can comment on the sketches.
peace and love
tom