Yeah definitely do not line with all plexiglass. That's going to be insanely expensive and hard to cut to specs. Just get a good polyurethane from home depot. They can help you find the correct one for the job. Let it dry thoroughly before you introduce any animals into it and allow it to vent fumes.
For disinfecting you can get some chlorhexidine from most reptile supply companies. A google search will yield a ton of results. Its used by vets and zoos predominately.