Hey @kbowman016, you should be able to create custom prototypes in landscape mode, but make sure you are using points, not pixels. Si if you're building for a retina iPad, use 1024x768, not 2048x1536.
Separately, are you able to get a prototype working without using assets (just using colored layers)? If so, do your assets have spaces in them? We have a known issue right now with encoding spaces in assets, so that might be causing the problem.