You would probably be time and expense ahead by starting with a flat deck trailer and building it to your specifications. You are going to run into major gut and rebuild issues with a travel trailer and it won't add much benefit in the end result.
Just off the top of my head--you'll need large water storage and food storage areas. A place to carry waste. Easy cleaning (and this might mean a floor decking that is impervious to water) where a hose and floor drain resides. You may wish to have a bathing sink where strays can be cleaned. In some cases you may wish to have a quarantine section where new-comers are housed until verified free from pests and disease. I would build with a total insulation system installed, something that is near impossible with an RV construction. You will want thick insulation and a vapor barrier to assist with HVAC and moisture. I can't imagine the amount of moisture from 40 animals but it is going to be huge. Large fans to transfer inside air.